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http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

https://elixir-europe.org/news/elixir-tools-and-data-services-registry-community-driven-curation-bioinformatics-resources

Elixir Interoperability Platform to help people and machines to discover, access, integrate and analyse biological data. Encourages life science community to adopt standardized file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. Bioinformatics resource registry that provides scientific and technical information about analytical tools and data services for bioinformatics. Gateway to databases and tools for life science data analysis.Provides comprehensive and up-to-date catalogue of resources that are interactive and downloadable, and that offer programmatic access. The registry also allows the community to upload their own resources to the registry following a simple log in procedure.

Proper citation: ELIXIR Tools and Data Services Registry (RRID:SCR_014556) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry

https://github.com/viromelab/tracespipe

Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data.

Proper citation: TRACESPipe (RRID:SCR_018831) Copy   

•   Source: SciCrunch Registry

https://robetta.bakerlab.org/

Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure.

Proper citation: Robetta (RRID:SCR_018805) Copy   

•   Source: SciCrunch Registry

https://inrae.github.io/ODAM/

Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users.

Proper citation: ODAM (RRID:SCR_018774) Copy   

•   Source: SciCrunch Registry

http://crdd.osdd.net/raghava/algpred/

Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes.

Proper citation: AlgPred (RRID:SCR_018780) Copy   

•   Source: SciCrunch Registry

https://nanopore.usegalaxy.eu/

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

Proper citation: NanoGalaxy (RRID:SCR_018912) Copy   

•   Source: SciCrunch Registry

https://github.com/HicServices/BadMedicine

Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes.

Proper citation: BadMedicine (RRID:SCR_018879) Copy   

•   Source: SciCrunch Registry

https://github.com/ylab-hi/ScanITD

Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation.

Proper citation: ScanITD (RRID:SCR_018886) Copy   

•   Source: SciCrunch Registry

https://github.com/davidebolo1993/TRiCoLOR

Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.

Proper citation: TRiCoLOR (RRID:SCR_018801) Copy   

•   Source: SciCrunch Registry

https://beikolab.cs.dal.ca/software/STAMP

Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups.

Proper citation: STAMP (RRID:SCR_018887) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

http://www.e-crisp.org/E-CRISP/

Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours.

Proper citation: E-CRISP (RRID:SCR_019088) Copy   

•   Source: SciCrunch Registry

http://enterobase.warwick.ac.uk/

Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.

Proper citation: EnteroBase (RRID:SCR_019019) Copy   

•   Source: SciCrunch Registry

http://dgenies.toulouse.inra.fr/

Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

Proper citation: D-GENIES (RRID:SCR_018967) Copy   

•   Source: SciCrunch Registry

https://nrdg.github.io/fracridge

Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.

Proper citation: fracridge (RRID:SCR_019045) Copy   

•   Source: SciCrunch Registry

https://github.com/medema-group/bigslice

Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data.

Proper citation: BiG-SLiCE (RRID:SCR_019130) Copy   

•   Source: SciCrunch Registry

https://github.com/slzarate/parliament2

Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data.

Proper citation: Parliament2 (RRID:SCR_019187) Copy   

•   Source: SciCrunch Registry

https://github.com/dmnfarrell/epitopepredict

Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported.

Proper citation: epitopepredict (RRID:SCR_019221) Copy   

•   Source: SciCrunch Registry