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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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 tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.
Proper citation: METAREP (RRID:SCR_011926) 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
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
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://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
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
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
http://www.reddit.com/r/bioinformatics/
A subreddit dedicated to bioinformatics, computational genomics and systems biology.
Proper citation: reddit (RRID:SCR_011983) Copy
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
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