【分析方法】生物信息学一些基本的常用软件

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楼主 2020-10-11 15:38:36
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简单罗列一些,主要是基于二代测序数据的群体基因组学常用软件。

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 Introduction to Circos, Features and Uses // CIRCOS Circular Genome Data Visualization

Mapping

BWA http://bio-bwa.sourceforge.net/

Maq http://maq.sourceforge.net/

stampy http://www.well.ox.ac.uk/project-stampy

Bowtie http://bowtie-bio.sourceforge.net/index.shtml

Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

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 Dindel: Accurate indel calls from short-read data

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/

Phylogenetic tree

fasttree http://www.microbesonline.org/fasttree/

RAxm l http://sco.h-its.org/exelixis/web/software/raxm l/index.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/

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

Transc riptome

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

来源:知乎

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