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301. ProbeMatch
Matches a large set of oligonucleotide sequences against a genome database using gapped alignments
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302. MetMap
Produces corrected site-specific methylation states from MethylSeq experiments and annotates unmethylated islands across the genome.
标签：DNA methylation
303. Rsolid
Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors
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304. Coral
Corrects sequencing errors in short read data via multiple alignments
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305. GAMES
GAMES (Genomic Analysis of Mutations Extracted by Sequencing) is a tool for mining and prediction of functional effect of mutation.
标签：SNP discovery, SNP Annotation,InDel discovery
306. BRCA-diagnostic
Computational screening test for BRCA1/2 mutants in human genomic DNA
标签：Personal genomics
307. SUTTA
De novo assembly algorithm for assembling bacterial genomes from second generation sequencing data
标签：De-novo assembly
308. FACS
Rapid and accurate classification of sequences as belonging or not belonging to a reference sequence.
标签：Metagenomics
309. ABMapper
Maps RNA-Seq reads to target genome considering possible multiple mapping locations and splice junctions
标签：Genomics, Transcriptomics
310. Meraculous
De novo genome assembler from short reads
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311. Metaxa
Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets
标签：Metagenomics, Phylogenetics,Sequence analysis, Community analysis
312. NucleR
nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling
标签：ChIP-on-chip, ChIP-Seq,Nucleosome Positioning,Epigenomics
313. GRS
Reference-based data compression for storage of resequencing data
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314. LobSTR
lobSTR is an alignment and genotyping tool for profiling short tandem repeats from next generation sequencing data
标签：Sequencing
315. FDM
Detects differential transcription in RNA-Seq data
标签：RNA-Seq Quantitation
316. T-lex
Here, we present a computational pipeline (T-lex) that uses NGS data to detect the presence/absence of annotated Transposable Element (TE) copies. T-lex can use data from a large number of strains and returns estimates of population frequencies of individual TE insertions in a reasonabl...
标签：Transposable Elements
317. SeqWare
SeqWare provides tools designed to support massively parallel sequencing technologies.
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318. GenomeView
GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Man...
标签：Genomics, Comparative genomics, Comparative transcriptomics,Transcriptomics, Gene annotation retrieval, Quality Control, Sequencing, Sequence analysis
319. SEWAL
Processing of deep sequencing data from in vitro selection experiments
标签：In vitro selection
320. CatchAll
Estimate ecological diversity with both parametric and non-parametric estimators.
标签：Population genetics,Metagenomics
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