Best Web-Based Bioinformatics Software of 2024

We build products with our in-house chemists, biologists and clients to deliver outstanding performance and scientific understanding. Chemaxon offers a wide range of products, including out-of-the box solutions for scientists and IT professionals. It also includes components that add extra functionality as well as integrations with 3rd-party software, such Microsoft Excel or KNIME. Chemaxon, a leading software provider, is trusted by more than one million users. Its industry-leading tools for scientific discovery include calculation, search, and drawing tools. Our applications are used widely in education and research in the life sciences. Our clients come from a wide range of industries. The majority of major pharmaceutical companies are among them. Our offices are located at Budapest, Basel and Boston, with distributors all over the world.

Pluto was founded in 2021 by the Wyss Institute of Harvard University. It has been a trusted partner for many life sciences organizations across the country, from biotech start-ups and public biopharma companies. Our cloud-based platform allows scientists to manage all their data, run bioinformatics analysis, and create interactive visualizations that are published-quality. The platform is being used for a variety of biological applications. These include preclinical and translational science research, cell and gene therapies and drug discovery and development.

Interactive visualizations and analytics allow you to explore hundreds of single-cell transcriptome datasets as well as your own data. The software supports multimodal omics (e.g. CITE-seq and spatial transcriptomic. Explore the world's largest database of single-cell expression interactively. Access and query insights derived from a single cell database of millions of cells. The database is fully annotated, with cell type labels and experimental meta-data. BBrowser does not just create a portal to published works. It is an end-toend solution for YOUR single-cell data. Import your fastq, count matrices or Seurat objects and reveal the biological stories within. With a powerful package of visualizations, analyses and an intuitive interface you can easily mine insights from any single-cell dataset. Import data from single-cell CRISPR or Perturb-seq. Guide RNA sequences can be queried.

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

Design and simulate cloning processes accurately. Test complex projects, catch mistakes before they happen, get the right constructs on the first try. Cloning becomes easier when you see what you're doing. The intuitive interface simplifies complex tasks by providing you with a clear view of your work. SnapGene automates the documentation so you don't need to. Share and view every sequence edit or cloning process that led to the final plasmid. Improve your core molecular biological procedures and your results. SnapGene Academy, our new online learning centre, will help you master SnapGene as well as key concepts in cloning. SnapGene Academy contains over 50 video tutorials, taught by experts in the field. This helps you improve your skills in multiple molecular biological courses. SnapGene 7.2 offers a new visualization for primer homodimer structure and enhancements to the file management. Tabs can be organized using drag-and-drop in multiple windows.

The toolkit was developed in the Data Sciences Platform of the Broad Institute. It offers a variety of tools, with a focus on variant detection and genotyping. Its powerful processing engine, high-performance computing capabilities and flexibility make it a great tool for any project. The GATK is a standard in the industry for identifying SNPs in RNAseq and germline DNA data. Its scope has now expanded to include somatic short variation calling, copy number (CNV), and structural variation (SV). The GATK includes not only the variant callers, but also many utilities that perform related tasks like processing and quality-control of high-throughput sequence data. It also bundles the Picard toolkit. These tools were designed primarily to process whole genomes and exomes generated by Illumina sequencing technology. However, they can be adapted for a variety other technologies and experimental design.

Galaxy is a web-based, open-source platform for data-intensive biomedical studies. Start here if you are a new Galaxy user or consult our support resources. Install Galaxy yourself by following the tutorial. You can choose from thousands of tools in the tool shed. This instance of Galaxy uses infrastructure generously provided to it by the Texas Advanced Computing Center. Additional resources are available primarily via the Jetstream2 cloud, via ACCESS and with support from National Science Foundation. Quantify, visualize and summarize mismatches from deep sequencing data. Build maximum-likelihood trees. Phylogenomic/evolutionary tree construction from multiple sequences. Using TN-93, combine matching reads to form clusters. Remove sequences that are within a certain distance of a cluster from a reference. Estimate gene essentiality scores using maximum-likelihood.

Cellenics can help you turn your single-cell sequencing data into meaningful insights. Cellenics is an open-source analytics tool developed by Harvard Medical School for single cell RNA sequencing data. Biomage hosts the community instance. It allows biologists to explore datasets of single-cells without having to write code, and helps scientists and informaticians work together more effectively. It can take you from count matrixes to publication ready figures in a matter of hours. It can also be seamlessly integrated into your workflow. It is fast, interactive and user-friendly. It's cloud-based and scalable. Cellenics, hosted by Biomage as a community instance, is free for academics with small/medium datasets (upto 500,000 cells). Over 3000 academic researchers use it to study cancer, cardiovascular health and developmental biology.

Improve team productivity and generate greater returns on research. Interactive data visualization allows you to share private and public data with other teams. Rosalind is a multi-tenant SaaS designed for scientists. Analyze, share, interpret, plan, validate and generate new hypotheses. Code-free visualization, AI-powered interpretation, best-in-class collaboration. ROSALIND is suitable for scientists of all levels, since it does not require any programming or bioinformatics knowledge. ROSALIND's powerful downstream analysis and collaborative capabilities make it a platform for discovery and data hub that connects experiment design, quality assurance, and pathway exploration. ROSALIND manages tens or thousands of cores of computing and petabytes in storage to dynamically scale each experiment up and down to deliver results. Share results instantly with other scientists around the world with audit tracking, so everyone can concentrate on interpretation and not the processing.

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.

Legacy R&D software can be a drain on scientific potential. It slows down R&D progress and scatters data between silos. Benchling is the industry's most trusted life sciences R&D cloud. All the tools you need to accelerate, measure, and forecast R&D, from discovery through bioprocessing, all in one place. A suite of seven applications that are natively unified and can be used to accelerate R&D at all levels. Open integration, codeless configuration, and dashboards that are tailored to your needs. For continued success, deep life science R&D and consulting expertise are essential. Benchling is a unified R&D platform that allows you to spend less time searching for data and more time working together in order to advance your research. Scientists, managers, executives, and researchers can optimize R&D output by having complete visibility into the experimental context, program performance, resource utilization, and program performance.

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.

StarDrop™, a comprehensive suite of integrated software, delivers the best in silico technology within a highly visual interface. StarDrop™, which allows seamless flow between the latest data, predictive modeling, and decision-making regarding the next round or synthesis, improves the speed, efficiency and productivity of the discovery process. A balance of different properties is essential for successful compounds. StarDrop™, which guides you through the multi-parameter optimization challenge, helps you target compounds with the highest chance of success. It also saves you time and resources by allowing you to synthesize fewer compounds and test them less often.

Partek bioinformatics software provides powerful visualization and statistical tools in an intuitive interface. Researchers of all levels can explore genomic data faster and more efficiently than ever before. We turn data into discovery®. Our intuitive interface makes it easy for scientists to perform sophisticated array and NGS analysis using pre-installed workflows. Public and custom statistical algorithms can be used together to quickly and accurately distill NGS data into biological insights. Genome browser, Venn diagrams and heat maps, as well as other interactive visualizations, show the biology of your next generation sequencing and array data in vivid color. Our Ph.D. scientists can be reached at any time to assist with your NGS analysis. This product is specifically designed for next-generation sequencing applications that require high-level computing. It offers flexible installation and management options.

Correlation Engine, an interactive omics database, places private omics data into a biological context by combining it with highly curated publicly available data. Correlation Engine, one of the largest databases in the world for life science research, provides researchers with unprecedented access and insight to a vast number of high-quality whole genome analyses. The knowledgebase allows for novel discoveries through the interrogation of billions of datapoints derived from standard analyses of whole genome studies. A suite of applications for determining biological context, a constantly growing library of curated datasets, and support of multiple species and multi-omic data sets. Use a simple graphical interface to leverage guided workflows and APIs. Accelerate the journey from omic to decision-making and gain access to more than 25,000 multi-omics studies that have been reanalyzed (from over 250.000 signatures).

Emedgene streamlines tertiary analyses for germline research and rare disease genomics. Emedgene was designed to speed up the time and certainty of user-defined variant interpretations, prioritizations, curations, and research reports. Automate your tertiary analyses with explainable AI and automation that supports genomes, exomes and virtual panels. Unify your NGS instruments and your IT systems in order to simplify and secure the entire workflow. With the latest knowledge graph options, curation abilities, and a team to support you, you can confidently keep up with evolving science, technologies, and demand. Automated workflows and explainable AI (XAI), which can be used to increase throughput without adding more staff, are a great way to do this. Implement a high-throughput WGS,WES, virtual panel or targeted panel workflow integrated into your lab's ecosystem.

Store, archive, and manage multi-omic data sets. Illumina Connected Analytics provides a secure platform for genomic data to operationalize informatics, and drive scientific insight. CWL and Nextflow allow you to easily import, build and edit workflows. Leverage DRAGEN bioinformatics pipelines. Organize your data in a safe workspace and share it with the world in a compliant way. Our platform allows you to keep your data in the cloud. Visualize and interpret data using a flexible analysis tool, such as JupyterLab Notebooks. Data warehouses allow you to aggregate, query and analyze sample data and population data. Scale analysis operations through the creation, validation, automation, and deployment of informatics pipelines. Reduce the time needed to analyze genomic data when quick results are a key factor. Enable comprehensive profiling for the identification of novel drug targets and biomarkers of drug response. Data can be transferred seamlessly from Illumina sequencing platforms.

Illumina DRAGEN Secondary Analysis is a comprehensive and accurate analysis of next-generation sequence data. Machine learning and graph reference genome drive unprecedented accuracy. Ultra-efficient workflow. Can process a whole 34x human genome in under 30 minutes using DRAGEN server version 4. Reduces FASTQ files up to 5x, resulting in an ultra-efficient workflow. Analyzes data from next-generation sequencing (NGS), including whole genomes, transcriptomes, methylomes and exomes. Available on the platform of your choice and scalable according to needs. DRAGEN analysis is the most accurate for germline and somatic mutation calling, as demonstrated by precisionFDA's industry challenges. DRAGEN analysis allows labs of any size and discipline to do more with genomic data. DRAGEN analysis is based on highly reconfigurable FPGA technology to provide hardware-accelerated implementations for genomic analysis algorithms.

Data management and simplified Bioinformatics are ideal for labs that are just getting started or for those who want to scale up their next-generation sequencing operations quickly. BaseSpace Sequence hub is an integral part of the BaseSpace Suite and is a direct extension to your Illumina instruments. BaseSpace Sequence hub allows you to manage your data with ease using a set of curated analysis apps. BaseSpace Sequence hub is powered by Amazon Web Services. Provides a secure environment. You can set up runs and monitor the quality of instrument runs. By converting sequence data into a standard format, and streaming it directly to the cloud, this tool promotes efficiency. Access to computing resources is available without the need for capital expenditures. Access to a variety of genomic analysis apps, whether provided by you, Illumina or third parties, increases organizational productivity.

Microsoft's experience and scale in managing exabyte-scale workloads can be used to reduce the need for you to manage your own data center. Microsoft Genomics on Azure gives you the performance and scalability that comes with a supercomputing facility of the highest caliber, all on demand. Take advantage of an MPI backend network that has a latency of under three microseconds, and a non-blocking throughput of 32 gigabits per seconds (Gbps). This backend network features remote direct memory access, which allows parallel applications to scale up to thousands of cores. Azure offers high memory and HPC class CPUs to help get results quickly. Scale up or down according to your needs and only pay for what you actually use. Azure's worldwide network of data centers can help you meet your compliance needs and address data sovereignty issues. Easy integration into your existing pipeline code with a REST API and simple Python client.

Software for fast, simple, and repeatable analysis of variants in gene panels, whole genomes, and exomes. VarSeq provides an intuitive and integrated software solution for tertiary analyses. VarSeq allows you to automate workflows and analyze variations for gene panels, whole genomes, and exomes. Our software makes it easier than ever to understand genomic data. VarSeq is a powerful software that provides a powerful filtering engine and annotation engine for sifting through large variant data. You can narrow down your list of variants quickly by using a series of filters. You can save the filters you have created after you have determined the parameters that are most effective for your analysis. This allows you to easily apply the same analysis on another dataset. VarSeq is ideal for high-throughput environments because the same automated workflow can apply to each batch of samples. Real-time filtering allows you to quickly prototype and fine-tune analysis workflows.

VSClinical allows the clinical interpretation based on ACMG & AMP Guidelines. The VSClinical workflow is guided by the American College of Medical Genetics guidelines for identifying and classifying causal variants in inherited disease risk, predisposition to cancer, and diagnosis of rare diseases. The ACMG/AMP Joint Guidelines for Variant Interpretation provide a set criteria to score variants, and place them in one of five classification tiers. The guidelines require a deep dive into the annotations and genomic context of each variant, as well as existing clinical assertions. VSClinical offers a customized workflow to score each relevant criteria, while also providing bioinformatics, literature and evidence gathered from clinical knowledgebases. VSClinical was designed to help variant scientists process variants efficiently.

GenomeStudio Software allows you to visualize and analyze data from Illumina array platforms. This powerful tool supports genotyping analysis of microarray datasets. Performance-optimized tools and a user-friendly graphical interface enable you to convert data into meaningful results quickly and easily. Analyze SNP/CNV data across 5,000,000 probes and markers. Detect outliers in sample data. Analyze differentially expressed genes across multiple genomes. Profile miRNA expression. Combine microRNA and mRNA data into one project. Single-base resolution detection of cytosine methylation. Identify methylation signatures throughout the entire genome. Illumina's goal is to use innovative technologies to analyze genetic variation and function. This will allow us to do studies that were impossible just a few short years ago. We believe it is vital to provide innovative, flexible, and scalable solutions that meet the needs of customers.

Polly allows you to harness the power of biomedical information. The Polly Platform allows you to scale batch jobs, workflows and visualization applications. Polly supports resource pooling, optimizes resource allocation based upon your usage requirements, and makes use of spot instances when possible. This results in optimization, efficiency, quicker response time, and lower costs for resources. Access a dashboard that allows you to monitor and track resource usage and costs in real-time. This will allow you to reduce overheads when resource management is done by your IT team. Polly's infrastructure is built around version control. Polly uses a combination dockers and interactive notebooks to ensure version control for your analyses and workflows. We have created a mechanism that allows data, code, and the environment to co-exist. This, along with cloud data storage and the ability for users to share projects, ensures reproducibility in every analysis.

A robust platform for automatic variant prioritization and clinical interpretation, as well as report generation, is essential to ensure efficient reporting of NGS-based clinical trials. Strand Omics, a cloud-based platform that is HIPAA-compliant and fast, drives our clinical diagnostics practice. It has been refined over 4 years with over 10,000 clinical reports and multiple peer reviewed publications. Strand Omics is a combination of bioinformatics algorithms and curated databases, visualization interfaces, and reporting capabilities. It offers specialized workflows that can be used for rare inherited disorders and somatic tumor profiling tests. The platform has over 10,000 variants curated to oncogenicity, 100 genes that are curated for druggability across multiple types of cancer, and 500 drugs that have been curated for evidence.