Results for "peak calling"
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...oud computing. Langmead et al, Genome Biol 10(11):R134, 2009 Full Text Calling SNPs without a reference s...epresentation of specific ontology categories among genes near ChIP-seq peaks Next-gen-seq software - a list...3774 days ago
Next generation sequencing in R or bioconductor environment
...q. chipseq The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. Documentation BayesPeak BayesPeak is a peak calling package for identifying DNA b...3619 days ago
Commercial and public next-gen-seq (NGS) software
...al University of Singapore. Perl/R. FindPeaks - perform analysis of ChIP-S...Tao Liu from Xiaole Shirley Liu's Lab. PeakSeq - PeakSeq: Systematic Scor...me to update this list. Alternate Base Calling Rolexa - R-based framework for base calling of Solexa data. Project publi...3513 days ago
Software packages for next gen sequence analysis
...University of Singapore. Perl/R. * FindPeaks - perform analysis of ChIP-S...Liu from Xiaole Shirley Liu's Lab. * PeakSeq - PeakSeq: Systematic Scor...e to update this list. Alternate Base Calling * Rolexa - R-based framework for base calling of Solexa data. Project publi...3237 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...ome data and performs variant calling an average of 3 times faster...utations, can perform variant calling at chrX; Input: VCF Output:...AM files, run through variant calling programs to generate intermed...igned sequence data- use MACS peak caller: BAM, BED, SAM, ELAND Ou...2903 days ago
- alignment: the mapping of a raw sequence read to a locat...s. The name Phred refers to the original Phred base-calling software, which first used an...ed read-depth translates into higher confidence for calling genomic variants. RNAME: ref...
2863 days ago
Genome Assembly Tools and Software - PART1 !!
The genome assemblers generally take a file of short seq...ther assembler) into longer contigs, by iteratively calling Vmatch and Trinity, until som...ermiKit 0.13 – De novo Assembly based Variant Calling pipeline for Illumina Short R...2680 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq data (uses pseudoa...al type of k-mers) Software (C++) http://www.csbio.unc.edu/rs/ Variant calling ChimeRScope Fusion transcri...2366 days ago
List of non-commercial NGS genotype-calling software
...ies crucially on the accurate calling of SNPs and genotypes. Recent...inty associated with genotype calling, and will especially benefit...Software for SNP and genotype calling using single individuals and...includes a mode for genotype calling IMPUTE2 http://mathgen.stats...2091 days ago
