生物信息学笔记

 

	表2-6.2 16S rDNA分析常用生物信息学工具
分析步骤	常用工具
质量控制	Fastx-Toolkit, FastQC ,Trimmomatic, Seqtk, NGS QC Toolkit, PrinSeq
16S rRNA数据库	Greengeens, Silva, RDP, nt
嵌合体分析	ChimeraSlayer, Uchime
聚类分析	QIIME, Uclust, UPARSE, Mothur, CD-hit, DOTUR, Trie
进化发育分析	ARB,PAML.Fast Tree,MEGA,Phylip,PAUP
功能分析	MEGAN ,PICRUST,Tax4Fim

 

	表2-6.6基因组拼组装常用生物信息学工具
软件名称	网址
SOAPdenovo Velvet Newhler ABySS Euler-SR ALLPATHS-LG QSRA SHARCGS Shorty SSAKE SparseAssembler	http:// soap, genomics. org. cn/ soapdenovo.html htlps：// github.com/ dzerbino/ velvet http://genepool, bio.ed.ac. uk/ Gene_Pool/454_software/ V ersion_2.6/ http:// www.bcgsc.ca/ platform/ bioi nfb/ software/ abyss http: //cblfs. cross-lfs. org/ index. php/Euler http://www.broadinstitute.org/software/allpaths-lg/blog/? page_id = 12 http ；//mocklerlab. org/ tools/2 http；// sharcgs.molgen.mpg.de/ download, shtml http:// www. cs. sunysb. edu/ ~ skiena/ shorty/utilities, html http ： // www. bcgsc. ca/ platform/ bi oinfb/ software/ ssake http:// sourceforge, net/ projects/ sparseassemblei/ files/ latest/download