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http://seqtracs.sourceforge.net/

Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.

Proper citation: SeqTRACS (RRID:SCR_013294) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/crossbow/index.shtml

A scalable software pipeline for whole genome resequencing analysis.

Proper citation: Crossbow (RRID:SCR_013306) Copy   

•   Source: SciCrunch Registry

http://libeep.sourceforge.net/

Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.

Proper citation: LIBEEP (RRID:SCR_009591) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/w2mhs/

An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis.

Proper citation: Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) Copy   

•   Source: SciCrunch Registry

http://cliiq.sourceforge.net/Home

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

Proper citation: CLIIQ (RRID:SCR_009972) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/excavatortool/

A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.

Proper citation: EXCAVATOR-tool (RRID:SCR_012766) Copy   

•   Source: SciCrunch Registry

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

An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.

Proper citation: Trowel (RRID:SCR_012890) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/oncosts/

Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.

Proper citation: Onco-STS (RRID:SCR_012990) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nxgview/

A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.

Proper citation: NxGview (RRID:SCR_012994) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamformatics/

Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.

Proper citation: Bamformatics (RRID:SCR_013041) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bsmapper/

Sequence mapper for bisulfite sequencing reads for DNA methylation studies.

Proper citation: BSmapper (RRID:SCR_012998) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mendelscan/

A software tool for prioritizing candidate variants in family-based studies of inherited disease.

Proper citation: MendelScan (RRID:SCR_013053) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/probeselect/

Software for selecting probes in heterogenous transcriptional sets.

Proper citation: ProbeSelect (RRID:SCR_012965) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqgenomebrowse/

Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data.

Proper citation: SeqGenome Browser (RRID:SCR_012970) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirdp/

A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

Proper citation: miRDeep-P (RRID:SCR_013026) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/quicktsaf/

Tool that compresses and decompresses fastq files.

Proper citation: KungFq (RRID:SCR_012979) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ncproseq/

Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.

Proper citation: ncPRO-seq (RRID:SCR_013031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcf2msat/

A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.

Proper citation: vcf2MSAT (RRID:SCR_013034) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fishingcnv/

A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.

Proper citation: FishingCNV (RRID:SCR_013038) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/msaprobs/

An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks.

Proper citation: MSAProbs (RRID:SCR_012982) Copy   

•   Source: SciCrunch Registry