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http://www.genestack.com

A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided.

Proper citation: Genestack (RRID:SCR_011885) Copy   

•   Source: SciCrunch Registry

https://www.globus.org/

Software-as-a-service for big data management offering fast, reliable, secure file transfer and sharing services to non-profit researchers. It combines state-of-the-art algorithms, data management tools, a graphical workflow environment, and an elastic computing infrastructure making it easy to manipulate, store, and share your data, no matter how big it gets.

Proper citation: Globus Genomics (RRID:SCR_011887) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/blast/html/megablast.html

Software that uses the greedy algorithm for nucleotide sequence alignment search.

Proper citation: Mega BLAST (RRID:SCR_011920) Copy   

•   Source: SciCrunch Registry

http://drive5.com/usearch/manual/uclust_algo.html

Algorithm that divides a set of sequences into clusters

Proper citation: UCLUST algorithm (RRID:SCR_011921) Copy   

•   Source: SciCrunch Registry

http://www.che.udel.edu/eXPatGen/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA).

Proper citation: eXPatGen (RRID:SCR_011922) Copy   

•   Source: SciCrunch Registry

http://ebardenovo.sourceforge.net/

Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Proper citation: EBARDenovo (RRID:SCR_011890) Copy   

•   Source: SciCrunch Registry

http://i.cs.hku.hk/~alse/hkubrg/projects/idba_tran/

An iterative De Bruijn Graph De Novo short read assembler for transcriptome.

Proper citation: IDBA-Tran (RRID:SCR_011891) Copy   

•   Source: SciCrunch Registry

https://www.softgenetics.com/NextGENe.php

Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support.

Proper citation: NextGENe (RRID:SCR_011859) Copy   

•   Source: SciCrunch Registry

http://www.csd.uwo.ca/~ilie/RACER/

A software program for correcting errors in sequencing data.

Proper citation: RACER (RRID:SCR_011852) Copy   

•   Source: SciCrunch Registry

http://cbio.ensmp.fr/~ahaury/svn/dream5/html/index.html

Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org).

Proper citation: TIGRESS (RRID:SCR_011977) Copy   

•   Source: SciCrunch Registry

https://trac.nbic.nl/narwhal/

Automates the primary analysis of massive parallel sequencing data.

Proper citation: NARWHAL (RRID:SCR_011858) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/orthagogue/

A software tool for high speed estimation of homology relations within and between species in massive data sets.

Proper citation: orthAgogue (RRID:SCR_011979) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene

An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.

Proper citation: SeqGene (RRID:SCR_011861) Copy   

•   Source: SciCrunch Registry

http://oqtans.org

It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.

Proper citation: Oqtans (RRID:SCR_011905) Copy   

•   Source: SciCrunch Registry

http://www.reddit.com/r/bioinformatics/

A subreddit dedicated to bioinformatics, computational genomics and systems biology.

Proper citation: reddit (RRID:SCR_011983) Copy   

•   Source: SciCrunch Registry

http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas

Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.

Proper citation: Genboree Workbench (RRID:SCR_011864) Copy   

•   Source: SciCrunch Registry

https://bioinf.eva.mpg.de/ibis/

An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads.

Proper citation: Ibis (RRID:SCR_011865) Copy   

•   Source: SciCrunch Registry

http://bayescall.sourceforge.net/

An efficient model-based base-calling algorithm for high-throughput sequencing.

Proper citation: naiveBayesCall (RRID:SCR_011866) Copy   

•   Source: SciCrunch Registry

http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: htseq-count (RRID:SCR_011867) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/

Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.

Proper citation: RNAseqViewer (RRID:SCR_011900) Copy   

•   Source: SciCrunch Registry