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http://sourceforge.net/projects/conifer/
Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
Proper citation: CoNIFER (RRID:SCR_013213) Copy
http://rdxplorer.sourceforge.net/
A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.
Proper citation: RDXplorer (RRID:SCR_013290) Copy
http://sourceforge.net/projects/pia2/
A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.
Proper citation: PIA (RRID:SCR_013267) Copy
A small tool for simulating sequence reads from a reference genome.
Proper citation: Wgsim (RRID:SCR_013269) Copy
http://soap.genomics.org.cn/SOAPdenovo-Trans.html
A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAPdenovo-Trans (RRID:SCR_013268) Copy
http://compbio.cs.ucr.edu/brat/
BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.
Proper citation: BRAT (RRID:SCR_013159) Copy
http://alumni.cs.ucr.edu/~liw/cem.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: CEM (RRID:SCR_013241) Copy
http://bioinfo.au.tsinghua.edu.cn/seqsite/
Software for detecting transcription factor binding sites from ChIP-seq data.
Proper citation: SeqSite (RRID:SCR_013243) Copy
http://www.bioconductor.org/packages/2.9/bioc/html/Repitools.html
Software tools for the analysis of enrichment-based epigenomic data.
Proper citation: Repitools (RRID:SCR_013242) Copy
http://www.bork.embl.de/software/smash/
A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies.
Proper citation: SmashCommunity (RRID:SCR_013245) Copy
http://sourceforge.net/projects/mirseq/files/
An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.
Proper citation: miRSeqNovel (RRID:SCR_013257) Copy
http://sourceforge.net/projects/ligmap/files/
A tool for structural biology and drug design.
Proper citation: AutoMap (RRID:SCR_013095) Copy
http://sourceforge.net/projects/dynamicprog/
A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.
Proper citation: DynamicProg (RRID:SCR_013217) Copy
http://www-rcf.usc.edu/~fsun/Programs/multiAlignFree/multiAlignFreemain.html
R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.
Proper citation: muliAlignFree (RRID:SCR_013188) Copy
http://www.bioconductor.org/packages//2.10/bioc/html/CancerMutationAnalysis.html
Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.
Proper citation: CancerMutationAnalysis (RRID:SCR_013181) Copy
Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.
Proper citation: BEADS (RRID:SCR_013229) Copy
http://sourceforge.net/projects/congrpe/
A de novo assembly algorithm for Next-Generation Sequencing technology.
Proper citation: CongrPE (RRID:SCR_013190) Copy
http://sourceforge.net/projects/callsim/
A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.
Proper citation: CallSim (RRID:SCR_013192) Copy
http://sourceforge.net/projects/sapas/
A RNA-seq method for polyA research.
Proper citation: SAPAS (RRID:SCR_013195) Copy
http://derisilab.ucsf.edu/index.php?software=105
An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.
Proper citation: HMMSplicer (RRID:SCR_013315) Copy
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