转载：http://www.zilhua.com/2081.html
参考资料：http://bioinfo.mc.vanderbilt.edu/NGS/software.htm
1. Mapping
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BFAST: A fast and accurate tool for mapping of short reads to reference sequences.
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BWA: A fast light-weighted tool that aligns short nucleotide sequences to a sequence database.
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Bowtie: An ultrafast, memory-efficient short read aligner.
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ELAND: A very fast alignment algorithms from Illumina company.
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MAQ: A software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.
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SHRiMP: A software package for aligning genomic reads against a target genome.
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SOAP: A tool package that provides full solution to next generation sequencing data analysis (including a alignment tool SOAPaligner/soap2 etc).
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SOLiD bioscope: A software package that is designed specifically to optimize the accuracy of the ABI SOLiD colorspace data.
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SWIFT: A software collection for fast index-based sequence comparison.
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TopHat: A spliced read mapper for RNA-Seq.
2. SNV Detection
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CASAVA: The internal assembler and variant caller Illumina company utilized.
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GATK: A multiple-sample, technology-aware SNV and indel caller.
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JointSNVMix: A probabilistic model for detection of somatic mutations in normal/tumour pair.
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SAMtools: A set of utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer.
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SNVMix: A tool for SNV calling based on probabilistic binomial mixture model.
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SOAPsnp: A tool for identifying SNVs by Beijing Genomics Institute (BGI).
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Strelka: A tool for somatic small-variant calling from sequenced tumor-normal sample pairs.
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SomaticSniper: A program to identify SNVs that are different between tumor and normal sample.
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VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.
3. Indel Detection
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Dindel: A program for calling small indels from short-read sequence data from Illumina platform.
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Pindel: A tool for identifying indels and structural variants at single-based resolution from next-generation sequence data.
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SplazerS: A tool for detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing.
4. Structural Variation Detection
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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.
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GASV: A tool for identifying and comparing structural variants by computing intersections of breakpoint regions.
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HYDRA: A tool for detecting structural variants in both unique and duplicated genomic regions.
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PEMer: A software package for detecting SVs from paired-end reads.
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R453Plus1Toolbox: An R/Bioconductor package for the analysis of Roche 454 sequencing data.
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SVMerge: A tool for SVs analysis by integrating calls from several existing SV callers.
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SVDetect: A tool for identifying structural variations from paired-end/mate pair data.
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VariationHunter: An tool for identifying structural variations from paired-end WGS data.
5. Copy Number Variation Detection
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CBS: An R package for detecting CNVs using sequencing data.
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CMDS: A population-based method for recurrent CNVs analysis from multiple samples.
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CNAseg: A tool for Identifying CNVs in cancer from NGS data.
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cnvHMM: A tool for CNVs analysis using Hidden Markov algorithm.
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CNVnator: A tool for CNV discovery and genotyping from depth of read mapping.
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FREEC: A tool for control-free CNVs detection using deep-sequencing data.
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RDXplorer: A tool for CNVs detection in whole human genome sequence data using read depth coverage.
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SegSeq: A tool for detecting CNVs from short sequence reads.
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VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.
6. Annotation
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ANNOVAR: An efficient software tool to use update-to-date information to functionally annotate genetic variants detected from diverse genomes.
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BreakSeq: A pipeline for annotation, classification and analysis of SVs at single nucleotide resolution.
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Seattle Seq: An server that provides annotation of SNVs.
7. Data Visualization
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Avadis: A software for visualizing and analyzing RNA-Seq data.
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CIRCOS: A software package for visualizing genomic events.
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IGV: A high-performance visualization tool for interactive exploration of next-generation sequencing data.
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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.
8. Fusion Gene Detection
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Avadis: A software for visualizing and analyzing RNA-Seq data.
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CIRCOS: A software package for visualizing genomic events.
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IGV: A high-performance visualization tool for interactive exploration of next-generation sequencing data.
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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.