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ABySS, Velvet, FastQC, SAMtools, SeqMonk, Newbler, BamTools, SeqMan NGen, CLCbio Genomics Workbench, Freebayes, Pindel, BEDTools, SeqMINER, STADEN, DNAA, MOSAIK, TMAP, Avadis NGS, IGV, Chipster, FREEC, BAMseek, Dindel, Ngs backbone, MACS, Breakway, Bcbio-nextgen, MagicViewer, Tablet, Stampy, SeqSolve, GASV, Savant Genome Browser, Genomatix Mining Station (GMS), GAMES, BamView, CopySeq, RTG Investigator, SAMStat, ChIP-Seq (application), BayesPeak, Atlas Suite, CLEVER, Contra, Ngs-pipeline, Syzygy, CNANorm, PALMapper, VarScan, Integrated Genome Browser

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