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http://compbio.bccrc.ca/software/snvmix/

Software designed to detect single nucleotide variants from next generation sequencing data.

Proper citation: SNVMix (RRID:SCR_013050) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/TurboNorm.html

Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Proper citation: TurboNorm (RRID:SCR_012963) 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://gmod.org/wiki/GBrowse_syn

A GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species.

Proper citation: GBrowse syn (RRID:SCR_012971) 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://www.bioconductor.org/packages/2.12/bioc/html/Ringo.html

Software package that facilitates the primary analysis of ChIP-chip data.

Proper citation: Ringo (RRID:SCR_012973) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ena/about/cram_toolkit

A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use.

Proper citation: CRAM (RRID:SCR_012975) 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

http://sourceforge.net/projects/qcreads/

Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms.

Proper citation: QcReads (RRID:SCR_013002) Copy   

•   Source: SciCrunch Registry

https://github.com/jstjohn/SeqPrep

A program to merge paired end Illumina reads that are overlapping into a single longer read.

Proper citation: SeqPrep (RRID:SCR_013004) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/phyloseq.html

Software for handling and analysis of high-throughput microbiome census data.

Proper citation: phyloseq (RRID:SCR_013080) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nsegata/phylophlan/wiki/Home

Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloPhlAn (RRID:SCR_013082) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hector454/

A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data.

Proper citation: HECTOR (RRID:SCR_013007) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/BayesPeak.html

Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.

Proper citation: BayesPeak (RRID:SCR_013011) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/ChIPseqR.html

Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments.

Proper citation: ChIPseqR (RRID:SCR_013016) Copy   

•   Source: SciCrunch Registry