Alternatives to BaseSpace Sequence Hub

The Illumina DRAGEN Secondary Analysis system offers precise, thorough, and highly efficient processing of next-generation sequencing data. Utilizing a graph reference genome alongside machine learning techniques, it achieves remarkable accuracy. The workflow is exceptionally streamlined, capable of completely analyzing a 34x whole human genome in approximately 30 minutes when using the DRAGEN server v4. Additionally, it enhances this workflow by compressing FASTQ file sizes by up to five times. This system is adept at analyzing a variety of NGS data types, including whole genomes, exomes, methylomes, and transcriptomes. It is designed to be compatible with the user's preferred platform and is scalable to meet varying requirements. DRAGEN analysis consistently ranks as a leader in accuracy for both germline and somatic variant detection, as evidenced by its performance in industry competitions conducted by precisionFDA. This advanced analysis solution empowers laboratories of all sizes and specialties to maximize the potential of their genomic datasets. Moreover, the implementation of highly adaptable field-programmable gate array (FPGA) technology allows DRAGEN to deliver hardware-accelerated genomic analysis algorithms, further enhancing its performance. Such advancements position DRAGEN as a vital tool in the ever-evolving field of genomics.

Geneyx Analysis offers an all-encompassing solution for managing next-generation sequencing (NGS) data, efficiently transforming FASTQ files into clinical reports tailored for both hospital and commercial laboratories. This cutting-edge platform incorporates machine learning and artificial intelligence capabilities to uncover new biomedical insights, enhancing diagnostic efficiency and reducing turnaround times. By delivering a fully transparent and user-friendly interface, Geneyx Analysis empowers clinicians and researchers with complete control over data interpretation and simplifies the challenges associated with managing in-house bioinformatics workflows. Users can customize protocols to suit various gene panels, exomes, and genomes, while our extensive annotation engine facilitates the analysis of all genetic variants, including structural and copy number variations, as well as regulatory elements. In combination, Geneyx Analysis streamlines the diagnostic journey from sequencer output to finalized report, while also serving as a valuable resource for the discovery of novel variants. This platform not only enhances clinical capabilities but also paves the way for groundbreaking research in genomics.

Manage, store, and collaborate on multi-omic datasets effectively. The Illumina Connected Analytics platform serves as a secure environment for genomic data, facilitating the operationalization of informatics and the extraction of scientific insights. Users can effortlessly import, construct, and modify workflows utilizing tools such as CWL and Nextflow. The platform also incorporates DRAGEN bioinformatics pipelines for enhanced data processing. Securely organize your data within a protected workspace, enabling global sharing that adheres to compliance standards. Retain your data within your own cloud infrastructure while leveraging our robust platform. Utilize a versatile analysis environment, featuring JupyterLab Notebooks, to visualize and interpret your data. Aggregate, query, and analyze both sample and population data through a scalable data warehouse, which can adapt to your growing needs. Enhance your analysis operations by constructing, validating, automating, and deploying informatics pipelines with ease. This efficiency can significantly decrease the time needed for genomic data analysis, which is vital when rapid results are essential. Furthermore, the platform supports comprehensive profiling to uncover novel drug targets and identify biomarkers for drug response. Lastly, seamlessly integrate data from Illumina sequencing systems for a streamlined workflow experience.

Universal Analysis Software (UAS) is a comprehensive platform that facilitates the analysis and management of forensic genomic data, making intricate bioinformatics tasks easier to navigate. This robust solution encompasses a variety of analysis modules that are compatible with all existing ForenSeq workflows, such as ForenSeq MainstAY, ForenSeq Kintelligence, ForenSeq DNA Signature Prep, ForenSeq mtDNA Whole Genome, and ForenSeq mtDNA Control Region. With UAS, users can swiftly generate FASTQ files, execute alignment processes, and identify forensically significant variants from next-generation sequencing (NGS) data. The software's extensive validation ensures highly dependable variant calls, providing precise outcomes in an accessible format without the burden of per-seat licensing fees. Tailored specifically for forensic analysts, UAS optimizes the management of base-by-base sequence data, offering a wide array of features that support everything from the efficient review of standard STR profiles to in-depth analysis of the most complex samples, thus enhancing the overall efficiency of forensic investigations.

Utilize GenomeStudio Software to visualize and analyze data produced on Illumina array platforms, which provides an advanced solution for genotyping microarray data. This robust toolset offers performance-enhanced capabilities and an intuitive graphical interface, allowing for swift and effortless transformation of data into insightful outcomes. You can examine SNP and CNV data through a comprehensive array of 5 million markers and probes, identify sample outliers, and investigate differentially expressed genes among various genomes. Additionally, it facilitates the profiling of miRNA expression and allows you to merge mRNA with microRNA data within a single project. The software also enables the detection of cytosine methylation at single-base resolution and helps in identifying methylation patterns throughout the genome. At Illumina, we are dedicated to leveraging groundbreaking technologies to advance the analysis of genetic variations and functions, paving the way for research that was once beyond reach. Our commitment is to provide innovative, adaptable, and scalable solutions that effectively address our customers' diverse needs. Ultimately, this focus on innovation ensures that we remain at the forefront of genetic research, facilitating discoveries that can transform our understanding of biology.

Eidogen-Sertanty's Target Informatics Platform (TIP) stands out as the pioneering structural informatics system and knowledgebase that empowers researchers to explore the druggable genome through a structural lens. By harnessing the burgeoning wealth of experimental protein structure data, TIP revolutionizes structure-based drug discovery, shifting it from a limited, low-throughput field to a dynamic and data-rich scientific discipline. It is specifically designed to connect the realms of bioinformatics and cheminformatics, providing drug discovery scientists with a repository of insights that are not only unique but also highly synergistic with the information available from traditional bio- and cheminformatics tools. The platform's innovative combination of structural data management with advanced target-to-lead calculation and analytical capabilities significantly enhances every phase of the drug discovery process. With TIP, researchers are better equipped to navigate the complexities of drug development and make informed decisions.

The innovative XetaBase platform streamlines tertiary analysis by aggregating, indexing, and enriching secondary genomic data, which facilitates ongoing re-evaluation to reveal valuable insights for research and clinical applications. By enhancing data management practices, XetaBase allows for the economical utilization of genomic information both in laboratories and clinical settings. The platform is designed to handle expansive genomic datasets, where increased volume and complexity lead to improved insights and outcomes. Built on the open-source OpenCB software framework, XetaBase is a genomic-native technology that addresses the demands for scalability, speed, and innovative re-interpretation in genomic medicine. Zetta Genomics provides an advanced genomic data management solution tailored for the era of precision medicine. This transformative platform eliminates outdated flat file methods, introducing actionable and relevant genomic data into both laboratory and clinical environments. Furthermore, XetaBase not only supports ongoing re-interpretation but also adapts effortlessly as databases expand to include more comprehensive genome sequences, ensuring that users stay at the forefront of genomic advancements.

Partek bioinformatics software offers robust statistical and visualization capabilities through a user-friendly interface that caters to researchers of varying expertise. This innovation allows users to navigate genomic data with unprecedented speed and ease, truly embodying our motto, "We turn data into discovery®." With pre-installed workflows and pipelines in a simple point-and-click format, even complex NGS and array analyses become accessible to all scientists. Our combination of custom and public statistical algorithms works seamlessly to transform NGS data into valuable biological insights. Engaging visual tools like genome browsers, Venn diagrams, and heat maps illuminate the intricacies of next-generation sequencing and array data with vibrant clarity. Additionally, our team of Ph.D. scientists is always available to provide support for NGS analyses whenever queries arise. Tailored to meet the demanding computational requirements of next-generation sequencing, the software also offers flexible options for installation and user management, ensuring a comprehensive solution for research needs. As a result, users can focus more on their research and less on technical challenges.

Combinatorial barcoding technology revolutionizes the outdated limitations of traditional single-cell methodologies. By eliminating the need for specialized instruments, it empowers researchers to make groundbreaking discoveries with ease. This innovation allows for the profiling of anywhere from 1,000 to 1 million cells or nuclei in a single experiment, driving forward unparalleled advancements in science. Evercode combinatorial barcoding technology significantly outperforms droplet-based methods, enabling researchers to increase the scale of their experiments without the constraints of previous technologies. Enjoy enhanced data quality while avoiding the complexities and requirements of outdated hardware. Conduct single-cell experiments using only a pipette and standard laboratory tools, simplifying the process and making it more accessible. The split-pool combinatorial barcoding technique facilitates scalable single-cell analysis without relying on any specialized instruments, making it easier than ever to achieve scalable sequencing. Each kit includes a comprehensive set of reagents and user-friendly analysis software, streamlining the entire workflow from start to finish for optimal efficiency. This technology not only enhances research capabilities but also fosters a new era of accessibility in scientific exploration.

g.nome is a cloud-native platform designed to offer efficient, scalable, and interoperable workflows tailored for next-generation sequencing analysis. It features a low-code/no-code approach to building pipelines, allowing users to access a curated library of pre-built workflows and toolkits. This empowers researchers to easily import their custom code, manage large datasets with confidence, and enhance collaboration among team members, regardless of their location. By utilizing g.nome, researchers can eliminate longstanding obstacles related to workflow languages, visibility of process flows, and quality assurance. Consequently, they can concentrate entirely on their scientific endeavors, as g.nome transforms the complexities of genomic workflows into streamlined, efficient processes. This innovative platform not only simplifies research but also fosters an environment where scientific inquiry can thrive unhindered.

The QIAGEN CLC Geneomics Workbench is a powerful tool that works for all workflows. It is easy to overcome data analysis challenges with cutting-edge technology, unique features and algorithms that are widely used by scientists in industry and academia. Bioinformatics software solutions that are user-friendly allow for comprehensive analysis and interpretation of your NGS data. This includes de novo assembly and transcriptome assembly, resequencing analysis, WES and targeted panel support, variant calling, variant calling, RNA–seq, ChIP–seq and DNA methylation analysis (bisulfite sequence analysis). You can analyze your RNA-seq (miRNA, smallRNA) and smallRNA (lncRNA), data using easy-to-use transcriptomics workflows that allow for differential expression analysis at both gene and transcript levels. QIAGEN CLC Genomics Workbench was designed to support a wide variety of NGS bioinformatics programs.

Geneious Prime enhances access to bioinformatics by converting raw datasets into intuitive visual representations that facilitate sequence analysis in a user-friendly manner. It offers straightforward sequence assembly along with the convenient editing of contigs. Users benefit from automatic gene prediction, motif identification, translation, and variant calling through its annotation features. It also allows for the genotyping of microsatellite traces using automated ladder fitting and peak calling, producing comprehensive tables of alleles. The platform showcases beautifully designed visualizations of annotated genomes and assemblies, presented in a customizable sequence view that enhances user experience. Furthermore, it supports powerful analyses of SNP variants, simplifies RNA-Seq expression evaluations, and assists in amplicon metagenomics. Users can also design and test PCR and sequencing primers while developing their own searchable primer database. Additionally, Geneious Biologics provides a versatile, scalable, and secure solution to optimize workflows for antibody analysis, enabling the creation of high-quality libraries and the selection of the most suitable therapeutic candidates. This integration of tools fosters greater efficiency and innovation in biological research.

Delve into a vast collection of meticulously curated single-cell transcriptome datasets, as well as your own, using dynamic visualizations and analytical tools. This software is versatile, accommodating multimodal omics, CITE-seq, TCR-seq, and spatial transcriptomics. Engage with the most extensive single-cell expression database globally, where you can access and extract insights from a repository featuring millions of fully annotated cells complete with cell type labels and experimental metadata. Beyond merely serving as a conduit to published research, BioTuring Browser functions as a comprehensive end-to-end solution tailored for your specific single-cell data needs. Easily import your fastq files, count matrices, or Seurat and Scanpy objects to uncover the biological narratives contained within. With an intuitive interface, you can access an extensive array of visualizations and analyses, transforming the process of extracting insights from any curated or personal single-cell dataset into a seamless experience. Additionally, the platform allows for the importation of single-cell CRISPR screening or Perturb-seq data, enabling users to query guide RNA sequences with ease. This functionality not only enhances research capabilities but also facilitates the discovery of novel biological insights.

Emedgene optimizes the workflows involved in tertiary analysis for rare disease genomics and various germline research endeavors. It is specifically built to enhance the speed and reliability of interpreting, prioritizing, curating, and generating research reports for user-defined variants. By incorporating explainable AI (XAI) and automation, Emedgene boosts efficiency across diverse analysis workflows, including genomes, exomes, virtual panels, and targeted panels. The platform facilitates the integration of laboratory processes and NGS instruments with IT systems, streamlining and securing the entire workflow. With continuous advancements in science, technology, and demand, Emedgene empowers users to stay current by offering cutting-edge knowledge graph features, curation tools, and expert support throughout their research journey. Furthermore, it allows laboratories to increase their throughput without the need for additional personnel, thanks to XAI and automated processes. Ultimately, Emedgene enables the deployment of high-throughput workflows for whole genome sequencing (WGS), whole exome sequencing (WES), virtual panels, or targeted panels that seamlessly fit into the digital framework of any lab. This comprehensive approach ensures that researchers can focus on their discoveries while relying on robust technological support.

Evo Designer is a cutting-edge tool created by the Arc Institute, harnessing the power of the Evo 2 genomic foundation model to aid in the generation and analysis of DNA sequences. Users can enter nucleotide sequences or select specific organisms, prompting the model to produce relevant DNA sequences tailored to their needs. This platform also offers detailed annotations of coding regions and provides 3D protein visualizations for prokaryotic sequences through ESMFold, enhancing the understanding of protein structures. In addition to these features, Evo Designer evaluates sequences by calculating their perplexity and per-nucleotide entropy, which helps researchers gauge the complexity and variability of the sequences they are working with. The Evo 2 model at the core of this tool has been trained on an impressive dataset of over 9 trillion nucleotides sourced from a wide variety of prokaryotic and eukaryotic genomes. Utilizing a sophisticated deep learning architecture, it models biological sequences with single-nucleotide precision and boasts a context window that can extend up to 1 million tokens, thereby ensuring high accuracy in sequence representation and analysis. This combination of features makes Evo Designer an invaluable resource for genetic research and exploration.

Created within the Data Sciences Platform at the Broad Institute, this comprehensive toolkit provides an extensive array of features primarily aimed at variant discovery and genotyping. With its robust processing engine and high-performance computing capabilities, it is equipped to manage projects of any magnitude. The GATK has established itself as the industry benchmark for detecting SNPs and indels in both germline DNA and RNA sequencing data. Its functionalities are now broadening to encompass somatic short variant detection as well as addressing copy number variations (CNV) and structural variations (SV). Besides the core variant callers, the GATK incorporates numerous utilities for executing associated tasks, including the processing and quality assurance of high-throughput sequencing data, and it comes bundled with the well-known Picard toolkit. Originally designed for exome and whole genome data generated via Illumina sequencing technology, these tools are versatile enough to be modified for use with various other technologies and study designs. As research evolves, the adaptability of the GATK ensures it remains relevant in diverse genomic investigations.

Transform your single-cell RNA sequencing data into actionable insights using Cellenics software, which is hosted by Biomage as a community instance of this open-source analytics tool developed at Harvard Medical School. This platform empowers biologists to delve into single-cell datasets without the need for coding, while facilitating collaboration between scientists and bioinformaticians. Within just a few hours, it can convert count matrices into publication-ready figures, integrating effortlessly into your existing workflow. Cellenics is designed to be fast, interactive, and user-friendly, as well as being cloud-based, secure, and scalable to meet various research needs. The community instance provided by Biomage is available at no cost for academic researchers working with smaller to medium-sized datasets, accommodating up to 500,000 cells. Currently, over 3000 academic researchers engaged in studies related to cancer, cardiovascular health, and developmental biology are utilizing this powerful tool. This collaborative environment not only enhances research capabilities but also accelerates the discovery process in various scientific fields.

OmicsBox, a leading bioinformatics tool, offers end-toend data analysis for genomes, transcriptomes and metagenomes. It also provides genetic variation studies. The application, which is used by leading private and public research institutes worldwide, allows researchers to process large and complicated data sets and streamline their analytical process. It is designed to be efficient, user-friendly and equipped with powerful tools to extract biological insight from omics data. The software is divided into modules, each of which has a set of tools and features designed to perform specific types of analyses, such as de novo genome assemblies, genetic variations analysis, differential expression analyses, taxonomic classifications, and taxonomic classes of microbiome, including the interpretation of results and rich visualizations. The functional analysis module uses the popular Blast2GO annotating methodology, making OmicsBox a great tool for non-model organisms research.

VSClinical facilitates the clinical analysis of genetic variants in accordance with ACMG and AMP guidelines. Its structured workflow supports adherence to the American College of Medical Genetics (ACMG) standards, which are essential for identifying and categorizing pathogenic variants related to inherited disease risk, cancer susceptibility, and rare disease diagnosis. The combined ACMG/AMP guidelines for variant interpretation establish a framework for scoring variants and categorizing them into one of five classification levels. Implementing these guidelines necessitates a thorough examination of annotations, genomic contexts, and pre-existing clinical insights for each variant. VSClinical streamlines this process by offering a customized workflow that evaluates each relevant criterion and supplies comprehensive bioinformatics, literature references, and clinical knowledgebase evidence to aid in the scoring and interpretation of variants. This innovative approach is designed to enhance the efficiency of variant scientists as they navigate the complexities of variant processing and analysis. Overall, VSClinical stands out as a vital tool for accelerating the understanding and classification of genetic variants in clinical settings.

Founded in order to improve lives through high-value care, the hc1 platform has become a leader in bioinformatics for precision prescribing and testing. The cloud-based hc1 high-value care platform® organizes large amounts of live data, including genomics and medications, to provide solutions that ensure the right patient receives the right test and prescription. The hc1 Platform is a platform that powers solutions that optimize diagnostic testing, prescribing, and patient care for millions of patients across the country. Visit www.hc1.com to learn more about the proven approach of hc1 to personalizing care and eliminating waste for thousands upon thousands of health systems, diagnostic labs, and health plans.

Correlation Engine serves as an engaging omics knowledgebase designed to situate private omics data within a rich biological framework alongside meticulously curated public datasets. Recognized as one of the most extensive biological databases globally, it offers life science researchers unparalleled access to an immense collection of high-quality whole-genome analyses, complemented by powerful scientific tools. This knowledgebase fosters groundbreaking discoveries by enabling the exploration of billions of data points sourced from standardized whole genome study analyses. It features an array of applications tailored for discerning biological context, a continuously expanding library of curated datasets, and versatility across various species and multi-omic datasets. Users can navigate through an intuitive graphical user interface that facilitates guided workflows, one-click applications, and application programming interfaces (APIs). By streamlining the transition from omic data to actionable insights, researchers can tap into over 25,000 multi-omics studies derived from more than 250,000 unique signatures that have undergone reanalysis, thereby enhancing their research capabilities even further.

Alissa Interpret serves as a comprehensive genomic data interpretation tool designed for enhancing clinical decision-making. It boosts your efficiency, reduces turnaround times, and ensures adherence to regulatory standards through its versatile CGH and NGS tertiary analysis platform dedicated to variant interpretation and reporting. When combined with Agilent’s top-tier SureSelect NGS reagents, the user-friendly secondary NGS analysis tool Alissa Reporter, Magnis walkaway automation, and TapeStation QC, Alissa Interpret achieves peak operational effectiveness for an efficient NGS data analysis process. Access to both external and internal curated variant knowledgebases is readily available, while the automated variant interpretation system speeds up CGH and NGS tertiary analysis. This single platform accommodates various genomic elements such as SNVs, InDels, CNVs, LOH, and fusions, and seamlessly integrates with your LIMS to eliminate any genomic data analysis delays. Furthermore, it fosters collaboration among peers, enabling the sharing of insights and ultimately enhancing diagnostic accuracy. By leveraging Alissa Interpret, laboratories can not only streamline their workflows but also elevate their overall diagnostic performance.

Rather than overseeing your own data centers, leverage Microsoft's extensive experience and scale in managing exabyte-level workloads. With Microsoft Genomics hosted on Azure, you gain access to the performance and scalability of a top-tier supercomputing facility, available on-demand in the cloud environment. Benefit from a backend network that boasts MPI latency of less than three microseconds and a non-blocking throughput of 32 gigabits per second (Gbps). This advanced network features remote direct memory access technology, allowing parallel applications to effectively scale to thousands of cores. Azure equips you with high memory and HPC-class CPUs designed to accelerate your results significantly. You can easily adjust your resources up or down according to your needs and only pay for what you consume, helping to manage costs efficiently. Address data sovereignty concerns with Azure's global network of data centers while ensuring compliance with regulatory requirements. Integration into your current pipeline is seamless, thanks to a REST-based API along with a straightforward Python client, making it easy to enhance your workflows. Additionally, this flexibility allows you to respond swiftly to changing demands in your projects.

We are at the forefront of precision medicine, alleviating the strain on healthcare systems through our innovative automated analysis, diagnosis, and treatment solutions that cater to healthcare providers and patients globally. Congenica emerged from groundbreaking research conducted at the Wellcome Sanger Institute and the UK's National Health Service. Our offerings integrate cutting-edge technology, top-tier automation, and artificial intelligence, allowing our distinct platform to be utilized across various human diseases where genomic information plays a crucial role in revealing actionable insights. As a digital health company, we specialize in software and solutions designed for the large-scale analysis and interpretation of genomic data. Our fully automated system, enhanced with robust APIs and machine learning capabilities, aims to lighten the load on specialist staff, improve case processing efficiency, speed up decision-making, and simplify reporting. Our platform is certified, accurate, and secure, empowering clinical decisions with the utmost confidence in the resulting clinical outcomes, and we continuously strive to innovate and expand our capabilities to meet the evolving needs of the healthcare landscape.

MEGA, which stands for Molecular Evolutionary Genetics Analysis, is an intuitive and highly capable software suite tailored for examining DNA and protein sequence information from various species and populations. It allows for both automated and manual alignment of sequences, the construction of phylogenetic trees, and the testing of evolutionary theories. The software employs an array of statistical approaches such as maximum likelihood, Bayesian inference, and ordinary least squares, making it indispensable for comparative sequence analysis and insights into molecular evolution. Additionally, MEGA includes sophisticated functionalities like real-time caption generation to clarify the findings and methodologies applied during analysis, alongside the maximum composite likelihood method for calculating evolutionary distances. The program is enhanced with powerful visual aids, including an alignment/trace editor and a tree explorer, while also supporting multi-threading to optimize processing efficiency. Furthermore, MEGA is compatible with several operating systems, such as Windows, Linux, and macOS, ensuring accessibility for a diverse user base. In summary, MEGA stands out as a comprehensive tool for researchers delving into the intricacies of molecular genetics.

Evo 2 represents a cutting-edge genomic foundation model that excels in making predictions and designing tasks related to DNA, RNA, and proteins. It employs an advanced deep learning architecture that allows for the modeling of biological sequences with single-nucleotide accuracy, achieving impressive scaling of both compute and memory resources as the context length increases. With a robust training of 40 billion parameters and a context length of 1 megabase, Evo 2 has analyzed over 9 trillion nucleotides sourced from a variety of eukaryotic and prokaryotic genomes. This extensive dataset facilitates Evo 2's ability to conduct zero-shot function predictions across various biological types, including DNA, RNA, and proteins, while also being capable of generating innovative sequences that maintain a plausible genomic structure. The model's versatility has been showcased through its effectiveness in designing operational CRISPR systems and in the identification of mutations that could lead to diseases in human genes. Furthermore, Evo 2 is available to the public on Arc's GitHub repository, and it is also incorporated into the NVIDIA BioNeMo framework, enhancing its accessibility for researchers and developers alike. Its integration into existing platforms signifies a major step forward for genomic modeling and analysis.

This complimentary software provides remarkable visual representations of your genomic information, allowing you to examine the specific activities at each base pair within your samples. GenomeBrowse operates as a native application on your desktop, eliminating the need to compromise on speed and quality while enjoying a consistent experience across different platforms. Designed with performance as a priority, it offers a quicker and more seamless browsing experience compared to any other genome browser on the market. Furthermore, GenomeBrowse is seamlessly integrated into the advanced Golden Helix VarSeq platform for variant annotation and interpretation. If you appreciate the visualization capabilities of GenomeBrowse, consider exploring VarSeq for tasks like filtering, annotating, and analyzing your data before leveraging the same interface for visualization. The software is capable of showcasing all your alignment data, and having the ability to view all your samples simultaneously can assist in identifying contextually significant findings. This makes it an invaluable tool for researchers seeking to gain deeper insights from their genomic data.

Galaxy serves as an open-source, web-based platform specifically designed for handling data-intensive research in the biomedical field. For newcomers to Galaxy, it is advisable to begin with the introductory materials or explore the available help resources. You can also opt to set up your own instance of Galaxy by following the detailed tutorial and selecting from a vast array of tools available in the tool shed. The current Galaxy instance operates on infrastructure generously supplied by the Texas Advanced Computing Center. Furthermore, additional resources are mainly accessible through the Jetstream2 cloud, facilitated by ACCESS and supported by the National Science Foundation. Users can quantify, visualize, and summarize mismatches present in deep sequencing datasets, as well as construct maximum-likelihood phylogenetic trees. This platform also supports phylogenomic and evolutionary tree construction using multiple sequences, the merging of matching reads into clusters with the TN-93 method, and the removal of sequences from a reference that are within a specified distance of a cluster. Lastly, researchers can perform maximum-likelihood estimations to ascertain gene essentiality scores, making Galaxy a powerful tool for various applications in genomic research.

Enhance research outcomes while boosting team efficiency by utilizing interactive data visualization to extend both private and public datasets among various teams. Rosalind stands out as the sole multi-tenant SaaS platform tailored for scientists, enabling the analysis, interpretation, sharing, planning, validation, and generation of new hypotheses with ease. It offers code-free visualization and employs AI for interpretation, fostering top-tier collaboration among users. Regardless of their expertise, scientists can leverage ROSALIND effectively, as it requires no programming or bioinformatics knowledge. The platform serves as a robust discovery tool and data hub, seamlessly integrating experiment design, quality control, and pathway analysis. ROSALIND's advanced infrastructure automatically orchestrates tens of thousands of compute cores and manages petabytes of storage, scaling resources dynamically for each experiment to ensure timely results. Furthermore, scientists can effortlessly share their findings with peers worldwide, complete with audit tracking to prioritize interpretation over data processing, thereby fostering a more collaborative research environment. This unique combination of features empowers researchers to focus on innovation and scientific discovery.

VarSeq is a user-friendly and efficient software designed for conducting variant analysis on gene panels, exomes, and complete genomes. This comprehensive software solution simplifies tertiary analysis, allowing users to effortlessly automate their workflows and examine variants across various genomic contexts. With VarSeq, the complexities of genomic data become more manageable, enabling researchers to easily navigate and interpret results. The software features a robust filtering and annotation system that helps users efficiently process extensive variant datasets. By employing a sequence of filters, you can swiftly refine your variant list to highlight those of greatest relevance. Once you establish effective parameters for your analysis, VarSeq allows you to save your filter configurations, facilitating the application of the same analytical approach to different datasets. This automated workflow can be consistently utilized across multiple sample batches, making VarSeq particularly suitable for high-throughput settings. Additionally, real-time filtering capabilities empower users to rapidly prototype and adjust analysis workflows according to their specific needs, enhancing the overall research experience. As a result, VarSeq significantly streamlines the variant analysis process for genetic studies.

Our worldwide data-sharing network produces actionable clinical insights from data aimed at enhancing patient outcomes on a global scale. SOPHiA GENETICS is dedicated to shaping the future of AI-enhanced medicine. By integrating various healthcare-omics data types, we are dismantling existing data barriers and creating machine learning models that yield insights capable of aiding healthcare professionals in elevating patient care. The updated interface, along with new features and advanced functionalities, will further expedite precision medicine workflows, bringing us closer to making data-driven healthcare accessible to all. Utilizing the power of AI and machine learning (ML), our cloud-based platform offers a secure and easily accessible space for the standardization, computation, and analysis of digital health data, which generates insights from intricate multimodal data sets that can significantly enhance diagnostic processes, therapy choices, analytical methods, and drug development initiatives. Moreover, our continuous evolution reflects our commitment to innovation in the healthcare sector.

The Bioconductor initiative is dedicated to creating and distributing open-source software designed for the accurate and reproducible analysis of biological datasets. We cultivate a welcoming and cooperative environment for developers and data scientists alike. The platform offers a wealth of resources aimed at enhancing the capabilities of Bioconductor. Whether you're looking for fundamental tools or sophisticated functionalities, our extensive tutorials, guides, and documentation ensure you have all the necessary support. Utilizing the R programming language, Bioconductor operates on an open-source and open development model. With biannual releases and a vibrant user community, it remains a vital resource in the field. Additionally, Bioconductor supplies Docker images for each release and offers assistance for its use within AnVIL. Established in 2001, Bioconductor is an essential open-source software resource extensively utilized in bioinformatics and biomedical research. It features over 2,000 R packages contributed by more than 1,000 developers, achieving over 40 million downloads annually. Furthermore, Bioconductor has been referenced in over 60,000 scientific articles, showcasing its significant impact on research and analysis in the biological sciences. This ongoing commitment to open-source collaboration continues to drive innovations in the field.

We are a biotechnology firm in the clinical stage, dedicated to unraveling biological complexities through the integration of cutting-edge innovations spanning biology, chemistry, automation, machine learning, and engineering, all aimed at revolutionizing drug discovery. Our approach allows for enhanced precision in biological manipulation with advanced techniques like CRISPR genome editing and synthetic biology. We also achieve reliable automation for intricate laboratory processes at an unprecedented scale through the use of sophisticated robotics. By employing neural network architectures, we conduct iterative analyses and draw insights from extensive, intricate datasets generated in-house. Furthermore, we are boosting the adaptability of high-performance computing capabilities through cloud-based solutions. Our initiative harnesses new technologies to foster continuous learning cycles around our datasets, establishing us as a next-generation biopharmaceutical enterprise. This is achieved through a harmonious integration of hardware, software, and data, all dedicated to the industrialization of drug discovery. We are transforming the conventional drug discovery pipeline and boast one of the most extensive, diverse, and in-depth pipelines among technology-driven drug discovery companies. Ultimately, our mission is to enhance the efficiency and effectiveness of drug development, paving the way for breakthrough therapies.

Choose two tailored cell groups by utilizing metadata to uncover their most significantly differentially expressed genes. Utilize the extensive collection of millions of cells from the integrated CZ CELLxGENE corpus for in-depth analysis. Conduct interactive examinations of datasets to investigate how gene expression patterns are influenced by spatial, environmental, and genetic variables through an intuitive no-code user interface. Gain insights into existing datasets or leverage them as a foundation to discover new cell subtypes and states. Census offers the capability to access any customized segment of standardized cell data available within CZ CELLxGENE, with opportunities for exploration in both R and Python. Delve into an interactive encyclopedia containing over 700 cell types that includes comprehensive definitions, marker genes, lineage information, and associated datasets all in one location. Additionally, you can browse and obtain hundreds of standardized data collections along with more than 1,000 datasets that detail the functionality of both healthy mouse and human tissues, enriching your research and understanding of cellular biology. This resource provides a valuable tool for researchers aiming to enhance their exploration of cellular dynamics and gene expression.

Azenta Life Sciences delivers robust, adaptable, and scalable informatics solutions for sample processing, designed to enhance lab systems' efficiency across multiple locations while incorporating comprehensive project and diagnostic management features. Our unmatched sample exploration and management services facilitate the acceleration of discovery, development, and delivery processes. The company provides cloud-based informatics solutions that streamline laboratory workflows and improve staff efficiency through standardized practices. Key software modules encompass the management of clinical trials, patient families, informed consent, sample storage, diagnostics, next-generation sequencing, and overall sample processing. Additionally, the system integrates seamlessly with external data sources and supports flexible integration with third-party systems and instruments, ensuring a cohesive laboratory environment. This innovative approach not only increases productivity but also enhances the overall quality of laboratory operations.

Loupe Browser stands out as a robust visualization tool, offering the user-friendly capabilities essential for delving into and interpreting 10x Genomics Chromium and Visium datasets. Additionally, the LoupeR package facilitates the transformation of Seurat objects into files compatible with Loupe Browser. The interactive features of the Loupe Browser interface are exemplified through its use of a lung squamous cell carcinoma dataset. Central to the user experience is the view panel, where individual points, each representing cell barcodes, are displayed across multiple projections. Each point typically corresponds to a single cell’s barcode, enabling focused analysis. The t-SNE plot generated by the cell ranger pipeline serves as the default projection, while alternative visualization options are also accessible. Users can effortlessly reposition the plot by dragging the mouse over the cells and can zoom in or out using the mouse wheel or trackpad. Moreover, as the mouse hovers over the plot, cluster labels become visible, which proves particularly beneficial when working with datasets that contain numerous precomputed clusters. This capability enhances the analytical experience, making it easier to identify and interpret complex data patterns.

NVIDIA® Parabricks® stands out as the sole suite of genomic analysis applications that harnesses GPU acceleration to provide rapid and precise genome and exome analysis for various stakeholders, including sequencing centers, clinical teams, genomics researchers, and developers of high-throughput sequencing instruments. This innovative platform offers GPU-optimized versions of commonly utilized tools by computational biologists and bioinformaticians, leading to notably improved runtimes, enhanced workflow scalability, and reduced computing expenses. Spanning from FastQ files to Variant Call Format (VCF), NVIDIA Parabricks significantly boosts performance across diverse hardware setups featuring NVIDIA A100 Tensor Core GPUs. Researchers in genomics can benefit from accelerated processing throughout their entire analysis workflows, which includes stages such as alignment, sorting, and variant calling. With the deployment of additional GPUs, users can observe nearly linear scaling in computational speed when compared to traditional CPU-only systems, achieving acceleration rates of up to 107X. This remarkable efficiency makes NVIDIA Parabricks an essential tool for anyone involved in genomic analysis.

HyperProtein is the latest offering from Hypercube, Inc., concentrating on the computational analysis of protein sequences. This innovative product not only examines one-dimensional sequences but also delves into the resulting three-dimensional structures of proteins. A key aspect of HyperProtein is its exploration of the intricate relationship between a protein's sequence and its structural form. In contrast to standalone software that targets specific functions like sequence alignment, HyperProtein combines a wide array of Bioinformatics and Molecular Modeling tools, providing a comprehensive approach to the science that begins with a protein sequence. By integrating these diverse tools, HyperProtein aims to enhance the understanding of protein functions and interactions at a molecular level, making it a valuable resource for researchers in the field.

ProximaX Sirius is a robust platform that combines a range of distributed and decentralized technologies, catering to both developers and enterprises. Its architecture features a network of multiple servers organized in a “hub and spoke” configuration, with the blockchain serving as the central “hub” and various service layers acting as “spokes.” These service layers incorporate functionalities such as peer-to-peer (P2P) and distributed storage, streaming, databases, and supercontracts, ensuring that all data—whether it’s for storage, messaging, or transactions—remains encrypted. The streaming capabilities cover diverse formats, including text, video, and voice. Moreover, ProximaX Sirius allows for the integration of additional service layers, which can enhance the platform’s capabilities by incorporating specialized services like artificial intelligence or distributed computing for tasks like genome sequencing. Notably, the performance of existing service layers is maintained even as new ones are added, akin to multiple sets of network server nodes operating simultaneously, all interconnected through the blockchain at the center. This design not only promotes scalability but also ensures that the system can adapt to evolving technological demands.

Qlucore Omics Explorer is designed to be user-friendly, eliminating the necessity to rely on bioinformatics experts for the exploration and analysis of your Omics and NGS datasets. This software serves as a do-it-yourself solution for next-generation bioinformatics in life sciences, plant and biotechnology sectors, and educational institutions. It features a robust and adaptable visualization-based data analysis tool that incorporates advanced statistical methods, yielding instant results and enabling immediate exploration and visualization of extensive data sets. Built to accommodate workflows that align with your research needs, it enhances the effectiveness of your studies. By merging real-time visualization with sophisticated statistical techniques and flexible selection options, you can promptly observe your findings. As a user, you have the autonomy to determine your own workflow and starting point, allowing for a customized exploration that aligns with your unique requirements. This level of control empowers researchers to tailor their analyses, ensuring that the software adapts seamlessly to diverse experimental designs.

The Genome Solution empowers businesses in various sectors to harness analytics for delivering tailored experiences to their end-users. This innovative solution enables companies to track customer interactions across multiple channels, including digital platforms, social media, and offline engagements, while integrating the internal data they possess based on behavioral traits, referred to as genomes. With a collection of over 5,000 pre-built customer genomes, it streamlines the process of data preparation and analysis, allowing enterprises to save up to 80% of the time typically spent on data setup. This efficiency not only accelerates data analysis but also lays the groundwork for advanced predictive and prescriptive analytics, fostering insights that are contextual and personalized to specific customer personas. Ultimately, the Genome Solution transforms how businesses understand and respond to their customers' needs in a rapidly evolving market.

We are a global provider for professional data storage solutions that are optimized for creative video, medical imaging and video surveillance. Our digital archive systems can store 100+ Petabytes of files and offer long-term, cost-effective, secure and long-term storage on RAID, LTO and optical cartridges. Our cloud solutions offer a global shared file system that makes your digital assets available to cloud computing and on-premises machines around the world.

Cease the struggle with cloud infrastructure and unreliable informatics tools; begin uncovering biological insights immediately. The scientific exploration process is hindered by the disjointed nature of tools utilized by biology and bioinformatics teams. To address this issue, we developed a unified bioinformatics platform that bridges the gap between wet lab and dry lab operations in the cloud, enabling teams to expedite their research and development efforts. You can easily import raw data from your cloud, your service provider, or your team's instruments with minimal hassle. Create and implement tailored bioinformatics workflows in various programming languages without the frustration of complex infrastructure management. Effortlessly execute any workflow while maintaining a comprehensive log of every analysis performed. Our platform features ready-to-use interactive visualizations for NGS data that allow you to create point-and-click plots with ease. Additionally, Latch seamlessly integrates with your organization’s AWS S3, granting access to hundreds of terabytes of data within a user-friendly organic filesystem. You can define bioinformatics workflows and dynamically generate no-code interfaces using Python, with adjustable compute and storage options to suit your needs. This innovative approach not only streamlines the research process but also fosters collaboration among teams, ultimately leading to more impactful scientific discoveries.

Clarity LIMS serves as a sophisticated laboratory information management system specifically tailored for genomics laboratories to effectively monitor samples and streamline workflows for enhanced laboratory efficiency. Beyond mere sample tracking, Clarity LIMS acts as a vital digital infrastructure for laboratory operations, encompassing every aspect from data and sample management to the oversight of personnel, equipment, and supplies. By standardizing and automating workflows, it significantly reduces the time required for processes and minimizes the likelihood of human error. This platform is designed to grow with your laboratory's needs, easily integrating new technologies and methodologies. Clarity LIMS also facilitates quicker laboratory operations through its easy-to-use implementation, offering preconfigured workflows for Illumina sample and library preparation kits, alongside quality control mechanisms that identify subpar samples. In addition, it aids in maintaining compliance with features such as electronic signatures, audit trails, reagent tracking, and robust privacy and security measures. Lastly, Clarity LIMS enhances precision through automation, incorporating built-in business logic and error-checking systems to ensure reliable results.

Efficiently address tissue heterogeneity and the intricacies of microenvironments using the GeoMx Digital Spatial Profiler (DSP), which stands out as the most versatile and powerful spatial multi-omic platform for examining both FFPE and fresh frozen tissue sections. Unique among spatial biology platforms, GeoMx allows for non-destructive profiling of RNA and protein expression across various tissue compartments and cell populations, supported by an automated and scalable workflow that seamlessly integrates with conventional histology staining. You can spatially profile the entire transcriptome along with over 570 protein targets, either separately or concurrently, utilizing sample inputs such as whole tissue sections, tissue microarrays (TMAs), or organoids. By choosing GeoMx DSP, you position yourself at the forefront of spatial biology for effective biomarker discovery and hypothesis validation. With the ability to determine the relevant boundaries, you can rely on biology-driven profiling that enables you to focus on the tissue microenvironments and cell types that hold the most significance for your research. This innovative approach ensures that your analyses are both comprehensive and tailored to the specific biological contexts of interest.

Designing and simulating cloning procedures with precision is essential for successful outcomes; testing complex projects can help identify potential errors in advance, ensuring that the correct constructs are generated on the first attempt. The process of cloning becomes significantly more manageable when users have clear visibility into their work, thanks to an intuitive interface that streamlines intricate processes. With SnapGene, documentation is automated, relieving users of the burden of manual record-keeping while allowing them to view and share every alteration made during sequence edits and cloning procedures that ultimately resulted in the final plasmid. Enhancing your core molecular biology techniques can lead to better experimental results, and by mastering SnapGene along with essential cloning concepts through the SnapGene Academy, you can elevate your expertise. This online learning platform features over 50 video tutorials conducted by experienced scientific professionals, enabling you to broaden your knowledge across a range of molecular biology subjects. Additionally, the recent SnapGene 7.2 update introduces improved visualization of primer homodimer structures and enhances file management, allowing for better organization of tabs across multiple windows through a user-friendly drag-and-drop feature. This makes it easier than ever to manage your cloning projects efficiently and effectively.

Founded in 2018, Seqera is a company headquartered in Spain that creates software called Seqera. Seqera is a type of bioinformatics software. Seqera includes phone support and online support. The Seqera software product is SaaS and On-Premise software. Seqera offers training via documentation, live online, webinars, in person sessions, and videos. Some competitors to Seqera include Pluto, LatchBio, and L7|ESP.

Cufflinks is a software tool that compiles transcripts, estimates their levels of abundance, and evaluates differential expression and regulation in RNA-Seq datasets. By accepting aligned RNA-Seq reads, it organizes these alignments into a streamlined representation of transcripts. The software then assesses the relative abundances of these transcripts based on the number of supporting reads, while also factoring in potential biases from library preparation methods. Initially created through a collaboration with the Laboratory for Mathematical and Computational Biology, Cufflinks aims to simplify the installation process by offering several binary packages that alleviate the often cumbersome task of building the software from source, which necessitates the installation of various libraries. This toolset encompasses multiple utilities tailored for analyzing RNA-Seq experiments, with some functionalities available independently and others designed to fit into a more comprehensive workflow. Overall, Cufflinks serves as a vital resource for researchers in the field of genomics, enhancing their ability to interpret RNA-Seq data effectively.

DNAnexus Titan™ is revolutionizing the field of genomics research and clinical workflows by offering reliable, high-performance data analysis solutions tailored for modern needs. Traditional informatics tools often struggle to cope with the increasing volumes of sequencing data generated today. Many research institutions and clinical diagnostic firms are grappling with the challenges posed by DIY systems, finding it laborious to establish, enhance, validate, and implement scalable pipelines. With DNAnexus Titan™, these hurdles are eliminated through a cohesive platform that integrates all data and workflows into a single environment, resulting in unmatched operational efficiencies. By entrusting us with the complexities of industry and region-specific security and compliance, you can focus on addressing the surging global demand for sequencing data without the burden of management challenges. Our platform not only simplifies the process but also enhances collaboration and accelerates scientific discovery.

The L7 Enterprise Science Platform (L7|ESP®) is a comprehensive platform designed to contextualize data and remove business silos through process orchestration. This all-in-one solution supports the digitalization of data and scientific processes within life sciences organizations. It includes native applications like L7 LIMS, L7 Notebooks, L7 MES, and L7 Scheduling. L7|ESP seamlessly integrates with third-party applications, lab instruments, and devices to consolidate all data into a unified model. Featuring a low-code/no-code workflow designer and numerous pre-built connectors, it ensures rapid implementation and full automation. Utilizing a single data model, L7|ESP enhances advanced bioinformatics, AI, and ML to provide new scientific and operational insights. L7|ESP addresses the data and lab management needs and challenges within the life sciences sector, specifically targeting: ● Research and Diagnostics ● Pharma and CDMO ● Clinical Sample Management Explore the L7 Resource Center for on-demand recordings, case studies, datasheets, and more: l7informatics dot com/resource-center