Month: November 2019
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Anvi’o 安装
Dependencies DIAMOND or NCBI’s blastp for search. MCL for clustering. muscle for alignment. easy install through conda: wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh chmod 777 Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh #在询问是否将conda加入环境变量的时候选择no cd miniconda3/bin/ chmod 777 activate . ./activate #添加频道 conda config –env –add channels conda-forge conda config –env –add channels bioconda conda create -n anvio-6 python=3.6 conda activate anvio-6…
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MLST细菌分型
多位点序列分型（multilocus sequence typing,MLST）是一种基于核酸序列测定的细菌分型方法。这种方法通过PCR扩增多个管家基因内部片段并测定其序列，分析菌株的变异。 依赖conda安装 conda install -c conda-forge -c bioconda -c defaults mlst mlst contigs.fa contigs.fa neisseria 11149 abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) mlst genomes/* genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3) genomes/strep.fasta.gz ssuis 1 aroA(1) cpn60(1) dpr(1) gki(1) mutS(1) recA(1) thrA(1) genomes/NC_002973.gbk lmonocytogenes 1 abcZ(3) bglA(1) cat(1) dapE(1) dat(3)…
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ARDB和VFDB数据库比对后筛选
python .py -i db.fasta -I blastresult.tab -o selected.txt -O filtered.txt blastresult.tab是根据P值sort后的文件 from __future__ import division import re import sys, getopt import operator from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.Alphabet import generic_nucleotide opts, args = getopt.getopt(sys.argv[1:], “hI:i:o:O:”) input_info1= “” input_info2= “” out_file1 = “” out_file2 = “” for op,…
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ARDB注释抗药基因
wget -c ftp://ftp.cbcb.umd.edu/pub/data/ARDB/ARDBflatFiles.tar.gz tar -zxvf ARDBflatFiles.tar.gz wget -c ftp://ftp.cbcb.umd.edu/pub/data/ARDB/ardbAnno1.0.tar.gz tar -zxvf ardbAnno1.0.tar.gz makeblastdb -in resisGenes.pfasta -dbtype prot -out ARDB vim genomeList.tab #目的蛋白序列路径 perl ardbAnno.pl