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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.
http://campagnelab.org/software/gobyweb/
Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.
Proper citation: GobyWeb (RRID:SCR_005443) Copy
http://www.computationalbioenergy.org/qc-chain.html
A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data.
Proper citation: QC-Chain (RRID:SCR_005438) Copy
https://github.com/laserson/vdj
Python package for analysing immune receptor sequences (antibodies and T cell receptors).
Proper citation: VDJ (RRID:SCR_005475) Copy
http://carringtonlab.org/resources/cashx
Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G.
Proper citation: CASHX (RRID:SCR_005477) Copy
http://sourceforge.net/p/treq/home/Home/
A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.
Proper citation: TreQ (RRID:SCR_005505) Copy
Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.
Proper citation: PiMS (RRID:SCR_011816) Copy
http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/
A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform.
Proper citation: Galaxy LIMS (RRID:SCR_011829) Copy
http://archimedes.cheme.cmu.edu/?q=gpublast
Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries.
Proper citation: GPU-BLAST (RRID:SCR_011820) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
A web-based tool used to search translated nucleotide databases using a translated nucleotide query.
Proper citation: TBLASTX (RRID:SCR_011823) Copy
An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more.
Proper citation: IGB (RRID:SCR_011792) Copy
http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
https://code.google.com/p/ngsplot/
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
Proper citation: ngs.plot (RRID:SCR_011795) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
http://pipmaker.bx.psu.edu/pipmaker/
PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
Proper citation: PipMaker and MultiPipMaker (RRID:SCR_011806) Copy
A generic sequence comparison tool for visualizing genome alignments both within and between species.
Proper citation: SynBrowse (RRID:SCR_011807) Copy
http://code.google.com/p/condetri/
Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.
Proper citation: ConDeTri (RRID:SCR_011838) Copy
http://www.cbcb.umd.edu/software/quake/
A software package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
Proper citation: Quake (RRID:SCR_011839) Copy
Software providing a framework for collecting, storing, and accessing data produced by a wide variety of experiments.
Proper citation: SBEAMS (RRID:SCR_011830) Copy
A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
Proper citation: Circos (RRID:SCR_011798) Copy
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