The common tools used in the NGS analysis

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.

  • 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.

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