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http://garm-meta-assem.sourceforge.net/

A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

Proper citation: GARM (RRID:SCR_006731) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/powermap/

Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.

Proper citation: PowerMap (RRID:SCR_006721) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/samscope/

A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.

Proper citation: Samscope (RRID:SCR_006715) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dmeas/

A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.

Proper citation: DMEAS (RRID:SCR_006679) 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/mirdeepstar/

An integrated application software tool for miRNA identification from RNA sequencing data.

Proper citation: miRDeep* (RRID:SCR_012960) 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