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http://sourceforge.net/projects/flexbar/

Flexible barcode and adapter removal for sequencing platforms.

Proper citation: Flexbar (RRID:SCR_013001) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/shrec-ec/

A bioinformatics tool for error correction of HTS read data.

Proper citation: SHREC (RRID:SCR_013009) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hictools/

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

Proper citation: hiCtools (RRID:SCR_013010) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/locas/

A software to assemble short reads of next generation sequencing technologies at low coverage.

Proper citation: LOCAS (RRID:SCR_013064) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/conifer/

Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.

Proper citation: CoNIFER (RRID:SCR_013213) Copy   

•   Source: SciCrunch Registry

http://rdxplorer.sourceforge.net/

A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.

Proper citation: RDXplorer (RRID:SCR_013290) Copy   

•   Source: SciCrunch Registry

http://nipy.org

Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.

Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pia2/

A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.

Proper citation: PIA (RRID:SCR_013267) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirseq/files/

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

Proper citation: miRSeqNovel (RRID:SCR_013257) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ligmap/files/

A tool for structural biology and drug design.

Proper citation: AutoMap (RRID:SCR_013095) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dynamicprog/

A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.

Proper citation: DynamicProg (RRID:SCR_013217) Copy   

•   Source: SciCrunch Registry

http://beads.sourceforge.net/

Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

Proper citation: BEADS (RRID:SCR_013229) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/congrpe/

A de novo assembly algorithm for Next-Generation Sequencing technology.

Proper citation: CongrPE (RRID:SCR_013190) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/callsim/

A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.

Proper citation: CallSim (RRID:SCR_013192) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sapas/

A RNA-seq method for polyA research.

Proper citation: SAPAS (RRID:SCR_013195) Copy   

•   Source: SciCrunch Registry

http://arrayoligosel.sourceforge.net/

Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.

Proper citation: ArrayOligoSelector (RRID:SCR_013494) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/splicegrapher/

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

Proper citation: SpliceGrapher (RRID:SCR_006657) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

•   Source: SciCrunch Registry