31、NGS 常用分析软件

转载：http://www.zilhua.com/2081.html

参考资料：http://bioinfo.mc.vanderbilt.edu/NGS/software.htm

1. 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.

2. 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.

3. 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.

4. Structural 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.

5. 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.

6. 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.

7. 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.

8. Fusion Gene Detection

• 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.