通用的軟件

perl,R, biopython, bioperl, bioconductor

序列比對(duì)

bowtie, bowtie2, bwa, blast, SOAPaligner,MUMmer, muscle, clustalw, blat, mega

過濾和質(zhì)控

FastQC, fastx-toolkit, NGS-QC-Toolkits, perlinhouse

轉(zhuǎn)錄組分析

Trinity, Oases, tophat, cufflinks, RSEM, eXpress, cumRound, DEseq, edgeR, misa, primer3_core, cd-hit

基因組組裝

ALLPATH-LG, SOAPdenovo, SOAPdenovo2,newbler,SSPACEs, velvet, ABySS, gapfiller, edena,

簡(jiǎn)化基因組

velvet, Rainbow

宏基因組16s

mothur, qiime, metasee, pandaseq, flash

基因芯片

TM4, J-Express,、Scanalyze,、KNNImpute

蛋白組分析

ReAdW, TPP, GPM

microRNA分析

targetscan, pstarget, miRanda,mfold,randfold, RNAhybrid,RNA22,miRNAkey, mirdeep2,RNAstructure

Chip-seq分析

cisgenome, macs

全基因組甲基化

PeakSeq, FindPeaks, BSMAP, BSSeeker

重測(cè)序分析

Bwa, SOAP, bowtie(bowtie2), Samtools, GATK, bedtools

基因組注釋

genescan, genemark, glimmers, AUGUSTUS

功能注釋

Blast2GO, Interproscan, PfamScan, HMMMER

重復(fù)序列注釋

RepeatMasker, RepeatModeler, RECON, RepeatScout,TRF

比較基因組學(xué)

CONTIGuator, Act, Mauve

群體遺傳學(xué)

HaploView,plink,gplink,tassel

其他

Circos, IGV, Tablet, Weblogo, Cytoscape, psRobot, promoter