二代测序数常用软件

作者：王理中
链接：https://www.zhihu.com/question/23566982/answer/25220599
来源：知乎
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Coding language
Perl http://www.perl.org/
Python https://www.python.org/
R http://www.r-project.org/

Plot
ggplot2 http://docs.ggplot2.org/current/
Circos http://circos.ca/

Mapping
BWA http://bio-bwa.sourceforge.net/
Maq (out-of-date) http://maq.sourceforge.net/
stamps (out-of-date) http://www.well.ox.ac.uk/project-stampy
Bowtie (out-of-date) http://bowtie-bio.sourceforge.net/index.shtml
Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
minimap https://github.com/lh3/minimap

SNP/Indel calling
samtools http://samtools.sourceforge.net/samtools.shtml
gatk http://www.broadinstitute.org/gatk/
angsd http://popgen.dk/angsd/index.php/Main_Page
soapsnp http://soap.genomics.org.cn/soapsnp.html
soapindel http://soap.genomics.org.cn/soapindel.html
pindel http://gmt.genome.wustl.edu/pindel/0.2.4/index.html
dindel http://www.sanger.ac.uk/resources/software/dindel/

Variant call format
about vcf format http://vcftools.sourceforge.net/specs.html
vcftools http://vcftools.sourceforge.net/index.html

Genotype phasing, imputation
beagle http://faculty.washington.edu/browning/beagle/beagle.html
impute2 http://genome.sph.umich.edu/wiki/IMPUTE2:_1000_Genomes_Imputation_Cookbook
phase http://stephenslab.uchicago.edu/software.html#phase
fastphase http://depts.washington.edu/fphase/Old/
SHAPEIT https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

Phylogenetic tree
fasttree http://www.microbesonline.org/fasttree/
RAxML http://sco.h-its.org/exelixis/web/software/raxml/index.html
Phylip http://evolution.genetics.washington.edu/phylip.html

Phylogen Programs http://evolution.genetics.washington.edu/phylip/software.html

Analysis tools
plink http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml
ngstools https://github.com/mfumagalli/ngsTools

LD
haploview http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

Structure analysis
frappe http://med.stanford.edu/tanglab/software/frappe.html
structure http://pritchardlab.stanford.edu/structure.html
admixture http://www.genetics.ucla.edu/software/admixture/
ngsAdmix http://www.popgen.dk/software/index.php/NgsAdmix

PCA
eigensoft http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html

Demographic history
dadi https://code.google.com/p/dadi/
psmc https://github.com/lh3/psmc
msmc https://github.com/stschiff/msmc
treemix treemix - Inference of population trees with admixture
fastsimcoal2 http://cmpg.unibe.ch/software/fastsimcoal2/
ChromoPainter/fineStructure/GLOBETROTTER http://www.paintmychromosomes.com/

Seletive sweeps
sweep http://www.broadinstitute.org/mpg/sweep/
ihs and xpehh http://hgdp.uchicago.edu/Software/
nSL http://cteg.berkeley.edu/software.html
SweepFinder http://people.binf.ku.dk/rasmus/webpage/sf.html
SweeD http://sco.h-its.org/exelixis/web/software/sweed/index.html
xp-clr http://genetics.med.harvard.edu/reichlab/Reich_Lab/Software.html

Transcriptome
Trinity http://trinityrnaseq.sourceforge.net/
velvet http://www.ebi.ac.uk/~zerbino/velvet/
Tophat http://tophat.cbcb.umd.edu/
cufflinks http://cufflinks.cbcb.umd.edu/
HISAT2 https://ccb.jhu.edu/software/hisat2/manual.shtml

Database
DDBJ http://www.ddbj.nig.ac.jp/index-e.html
ENA http://www.ebi.ac.uk/ena/home
NCBI http://www.ncbi.nlm.nih.gov/
ensembl http://asia.ensembl.org/index.html
ensembl plant http://plants.ensembl.org/index.html
KEGG http://www.genome.jp/kegg/
GO http://www.geneontology.org/

GWAS
FAST-LMM http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/
GAPIT https://groups.google.com/forum/#!forum/gapit-forum
EMMAX http://csg.sph.umich.edu/kang/emmax/download/index.html

RAD-seq
Stacks http://catchenlab.life.illinois.edu/stacks/manual/

SNP annotation
SNPeff http://snpeff.sourceforge.net/SnpEff_manual.html#intro
NGS-SNP http://www.ualberta.ca/~stothard/downloads/NGS-SNP/
ANNOVAR http://annovar.openbioinformatics.org/en/latest/user-guide/startup/

Protein functional effects
PolyPhen-2 http://genetics.bwh.harvard.edu/pph2/