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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://www.r-project.org/

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy   

•   Source: SciCrunch Registry

https://github.com/benedictpaten/pecan

A Java consistency based multiple sequence alignment software program.

Proper citation: Pecan (RRID:SCR_001909) Copy   

•   Source: SciCrunch Registry

http://www.agcol.arizona.edu/software/tcw/

Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.

Proper citation: TCW (RRID:SCR_001875) Copy   

•   Source: SciCrunch Registry

https://github.com/JialiUMassWengLab/TEMP

Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

Proper citation: TEMP (RRID:SCR_001788) Copy   

•   Source: SciCrunch Registry

https://github.com/nicolazzie/AffyPipe

An open-source software pipeline for Affymetrix Axiom genotyping workflow.

Proper citation: AffyPipe (RRID:SCR_002032) Copy   

•   Source: SciCrunch Registry

https://github.com/adrlar/CanSNPer

Software that is a hierarchical genotype classifier of clonal pathogens.

Proper citation: CanSNPer (RRID:SCR_001980) Copy   

•   Source: SciCrunch Registry

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

Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.

Proper citation: Ray (RRID:SCR_001916) 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://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