标题：NGS常用分析软件有哪些？
Mapping
BFAST: A fast and accurate tool for mapping of short reads to reference sequences.
BWA: A fast light-weighted tool that aligns short nucleotide sequences to a sequence database.
Bowtie: An ultrafast, memory-efficient short read aligner.
ELAND: A very fast alignment algorithms from Illumina company.
MAQ: A software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.
SHRiMP: A software package for aligning genomic reads against a target genome.
SOAP: A tool package that provides full solution to next generation sequencing data analysis (including a alignment tool SOAPaligner/soap2 etc).
SOLiD bioscope: A software package that is designed specifically to optimize the accuracy of the ABI SOLiD colorspace data.
SWIFT: A software collection for fast index-based sequence comparison.
TopHat: A spliced read mapper for RNA-Seq.
SNV Detection
CASAVA: The internal assembler and variant caller Illumina company utilized.
GATK: A multiple-sample, technology-aware SNV and indel caller.
JointSNVMix: A probabilistic model for detection of somatic mutations in normal/tumour pair.
SAMtools: A set of utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer.
SNVMix: A tool for SNV calling based on probabilistic binomial mixture model.
SOAPsnp: A tool for identifying SNVs by Beijing Genomics Institute (BGI).
Strelka: A tool for somatic small-variant calling from sequenced tumor-normal sample pairs.
SomaticSniper: A program to identify SNVs that are different between tumor and normal sample.
VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.
InDel Detection
Dindel: A program for calling small indels from short-read sequence data from Illumina platform.
Pindel: A tool for identifying indels and structural variants at single-based resolution from next-generation sequence data.
SplazerS: A tool for detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing.
Structure Variation Detection
BreakDancer: A tool for detecting five types of SVs (insertions, deletions, inversions, inter- and intra-chromosomal translocations) from next generation paired-end sequencing reads.
CREST: A software that uses the soft-clipped reads to directly map the breakpoints of SVs.
GASV: A tool for identifying and comparing structural variants by computing intersections of breakpoint regions.
HYDRA: A tool for detecting structural variants in both unique and duplicated genomic regions.
PEMer: A software package for detecting SVs from paired-end reads.
R453Plus1Toolbox: An R/Bioconductor package for the analysis of Roche 454 sequencing data.
SVMerge: A tool for SVs analysis by integrating calls from several existing SV callers.
SVDetect: A tool for identifying structural variations from paired-end/mate pair data.
VariationHunter: An tool for identifying structural variations from paired-end WGS data.
Copy Number Variation Detection
CBS: An R package for detecting CNVs using sequencing data.
CMDS: A population-based method for recurrent CNVs analysis from multiple samples.
CNAseg: A tool for Identifying CNVs in cancer from NGS data.
cnvHMM: A tool for CNVs analysis using Hidden Markov algorithm.
CNVnator: A tool for CNV discovery and genotyping from depth of read mapping.
FREEC: A tool for control-free CNVs detection using deep-sequencing data.
RDXplorer: A tool for CNVs detection in whole human genome sequence data using read depth coverage.
SegSeq: A tool for detecting CNVs from short sequence reads.
VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.
Annotation
ANNOVAR: An efficient software tool to use update-to-date information to functionally annotate genetic variants detected from diverse genomes.
BreakSeq: A pipeline for annotation, classification and analysis of SVs at single nucleotide resolution.
Seattle Seq: An server that provides annotation of SNVs.
Data Visualization
Avadis: A software for visualizing and analyzing RNA-Seq data.
CIRCOS: A software package for visualizing genomic events.
IGV: A high-performance visualization tool for interactive exploration of next-generation sequencing data.
Pairoscope: A software package for generating diagrams indicating the relationship of paired end sequencing reads, is most useful for visualizing translocations.
UCSC Genome Browser: A genome browser that provide precise access to sequence and annotation data for any genomic region of specific interest.
Fusion Gene Detection
BreakFusion: A tool to identify gene fusions from paired-end RNA-Seq data.
Chimerascan: A software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.
Comrad: A tool to identify aberrant transcripts and associated rearrangements using low coverage genome data.
[defuse](http://sourceforge.net/apps/me ... _Page "Main_Page"): A software for discovering gene fusion from RNA-Seq data.
FusionAnalyser: A software for detecting gene fusions from paired-end RNA-Seq data.
FusionHunter: A tool to identify fusion transcripts from transcriptional analysis of paired-end RNA-seq.
FusionMap: A software to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies.
FusionSeq: A tool to identify fusion transcripts from paired-end RNA-sequencing.
nFuse: A tool for detecting fusion transcripts and associated complex genomic rearrangements from matched RNA-seq and whole genome shotgun sequencing.
SnowShoes-FTD: A tool to find fusions from RNA-Seq data.
ShortFuse: A software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.
TopHat-Fusion: A software with the ability to align reads across fusion points.
Trans-ABySS: A software to analyses ABySS-assembled contigs from shotgun transcriptome data.
来源：知因