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http://mrsfast.sourceforge.net/

A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Proper citation: mrsFAST (RRID:SCR_003128) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/hyden/

Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

Proper citation: HYDEN (RRID:SCR_003126) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry

https://github.com/hangelwen/miR-PREFeR

An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

Proper citation: miR-PREFeR (RRID:SCR_003353) Copy   

•   Source: SciCrunch Registry

http://www.pictar.org

An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets

Proper citation: PicTar (RRID:SCR_003343) Copy   

•   Source: SciCrunch Registry

https://github.com/mozack/abra

Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).

Proper citation: Assembly Based ReAligner (RRID:SCR_003277) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html

Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.

Proper citation: NormqPCR (RRID:SCR_003388) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/popoolation/

A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

Proper citation: PoPoolation (RRID:SCR_003495) Copy   

•   Source: SciCrunch Registry

http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

•   Source: SciCrunch Registry

http://jexpress.bioinfo.no/site/

Gene expression analysis software using Java.

Proper citation: J-Express (RRID:SCR_003609) Copy   

•   Source: SciCrunch Registry

http://cakesomatic.sourceforge.net/

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

Proper citation: Cake (RRID:SCR_002133) Copy   

•   Source: SciCrunch Registry

https://github.com/mpyatkov/sbars

Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.

Proper citation: SBARS (RRID:SCR_002371) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html

A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.

Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/polyphred/

Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.

Proper citation: PolyPhred (RRID:SCR_002337) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isa2/

A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.

Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy   

•   Source: SciCrunch Registry

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

A fast parallel error correction tool for short reads.

Proper citation: CUDA-EC (RRID:SCR_001090) Copy   

•   Source: SciCrunch Registry

http://131.174.198.125/bioinfo/gimmemotifs/

Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GimmeMotifs (RRID:SCR_001146) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rbsurv.html

Software package that selects genes associated with survival.

Proper citation: rbsurv (RRID:SCR_001175) Copy   

•   Source: SciCrunch Registry

https://github.com/FelixKrueger/Sherman

Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.

Proper citation: Sherman (RRID:SCR_001294) Copy   

•   Source: SciCrunch Registry