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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
An open cloud company with performance Cloud Servers that offer 100% SSD storage & 10Gb Ethernet networking for your demanding applications.
Proper citation: Rackspace (RRID:SCR_011875) Copy
A general-purpose full virtualizer for x86 and AMD64/Intel64 hardware, targeted at server, desktop and embedded use.
Proper citation: VirtualBox (RRID:SCR_011876) 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
Software that virtualizes computing, from the data center to the cloud to mobile devices, to help customers be more agile, responsive, and profitable.
Proper citation: VMware (RRID:SCR_011878) 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
A cloud-based platform to support genomics at your organization.
Proper citation: DNAnexus (RRID:SCR_011884) Copy
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
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
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
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
http://ebardenovo.sourceforge.net/
Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Proper citation: EBARDenovo (RRID:SCR_011890) Copy
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
http://www.csd.uwo.ca/~ilie/RACER/
A software program for correcting errors in sequencing data.
Proper citation: RACER (RRID:SCR_011852) Copy
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
Automates the primary analysis of massive parallel sequencing data.
Proper citation: NARWHAL (RRID:SCR_011858) Copy
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
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
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
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