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http://transcriptome.ens.fr/eoulsan/
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
Proper citation: Eoulsan (RRID:SCR_011901) Copy
A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.
Proper citation: FX (RRID:SCR_011902) Copy
http://utgenome.org/index.html
An open-source software for developing personalized genome browsers that work in web browsers.
Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy
http://www.cisd.ethz.ch/software/openBIS
Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics
Proper citation: openBIS (RRID:SCR_011815) Copy
Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data.
Proper citation: Explicet (RRID:SCR_011937) Copy
An online toolbox for metagenomic data visualization.
Proper citation: MetaSee (RRID:SCR_011938) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
http://www.ebi.ac.uk/Tools/msa/kalign/
A fast and accurate multiple sequence alignment algorithm.
Proper citation: Kalign (RRID:SCR_011810) Copy
http://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) Copy
http://mafft.cbrc.jp/alignment/server/
Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
Proper citation: MAFFT (RRID:SCR_011811) Copy
http://bioen-compbio.bioen.illinois.edu/PSAR-Align/
Software for improving multiple sequence alignment using probabilistic sampling.
Proper citation: PSAR-Align (RRID:SCR_011814) Copy
http://www.csd.uwo.ca/~ilie/HiTEC/
Accurate error correction in high-throughput sequencing data.
Proper citation: HiTEC (RRID:SCR_011826) Copy
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
https://bioinf.eva.mpg.de/patman/
Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PatMaN (RRID:SCR_011821) Copy
http://bix.ucsd.edu/projects/hammer/
A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Hammer (RRID:SCR_011825) Copy
http://metavelvet.dna.bio.keio.ac.jp/
Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.
Proper citation: MetaVelvet (RRID:SCR_011915) Copy
http://swes.cals.arizona.edu/maier_lab/kartchner/documentation/index.php/home/docs/newbler
A software package for de novo DNA sequence assembly.
Proper citation: Newbler (RRID:SCR_011916) Copy
http://omics.informatics.indiana.edu/GeneStitch/
Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.
Proper citation: GeneStitch (RRID:SCR_011910) Copy
http://cs.stanford.edu/group/genovo/
Software for a novel de novo sequence assembler that discovers likely sequence reconstructions under the model.
Proper citation: Genovo (RRID:SCR_011911) Copy
https://hci-bio-app.hci.utah.edu/gnomex/
A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets.
Proper citation: GNomEx (RRID:SCR_011805) Copy
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