mlst這個軟件顧名思義就是做mlst的，需要的只是fasta,gbk,embl文件。
安裝當(dāng)然還是conda
conda install -c bioconda mlst
輸入
mlst -h
查看用法和參數(shù)
USAGE
% mlst --list 列出所有可以分析的細菌種屬#
% mlst [options] <contigs.{fasta,gbk,embl}[.gz] 自動選擇所用種屬
% mlst --scheme <scheme> <contigs.{fasta,gbk,embl}[.gz]> 指定種屬
參數(shù)很多，常用的如下：
--scheme 指定需要的種屬，如ecoli (可用--list查看）
--legacy 傳統(tǒng)的輸出方式輸出結(jié)果
--csv 輸出一個csv文件，方便使用excel后續(xù)處理
--threads 分析所用線程數(shù)量
查看現(xiàn)在支持的細菌種屬
mlst --list
abaumannii abaumannii_2 achromobacter aeromonas aphagocytophilum arcobacter bbacilliformis bcc bcereus bhampsonii bhenselae bhyodysenteriae bintermedia blicheniformis bordetella borrelia bpilosicoli bpseudomallei brachyspira brucella bsubtilis campylobacter cbotulinum cconcisus cdifficile cdiphtheriae cfetus cfreundii chelveticus chlamydiales chyointestinalis cinsulaenigrae clanienae clari cmaltaromaticum cronobacter csepticum csputorum cupsaliensis dnodosus ecloacae ecoli ecoli_2 edwardsiella efaecalis efaecium fpsychrophilum ganatis hcinaedi hinfluenzae hparasuis hpylori hsuis kaerogenes kkingae koxytoca kpneumoniae leptospira leptospira_2 leptospira_3 liberibacter lmonocytogenes lsalivarius mabscessus magalactiae mbovis mcanis mcaseolyticus mcatarrhalis mhaemolytica mhyopneumoniae mhyorhinis miowae mmassiliense mplutonius mpneumoniae msynoviae mycobacteria neisseria orhinotracheale otsutsugamushi pacnes paeruginosa pdamselae pfluorescens pgingivalis plarvae pmultocida_multihost pmultocida_rirdc ppentosaceus pputida psalmonis ranatipestifer rhodococcus sagalactiae saureus sbsec scanis sdysgalactiae senterica sepidermidis sgallolyticus shaemolyticus shominis sinorhizobium slugdunensis smaltophilia soralis spneumoniae spseudintermedius spyogenes ssuis sthermophilus sthermophilus_2 streptomyces suberis szooepidemicus taylorella tenacibaculum tpallidum ureaplasma vcholerae vcholerae2 vibrio vparahaemolyticus vtapetis vvulnificus wolbachia xfastidiosa yersinia ypseudotuberculosis yruckeri
以ncbi上3株大腸桿菌為例，以傳統(tǒng)模式輸出結(jié)果到csv文件：
mlst --scheme ecoli --legacy --csv *.fna > mlst.csv
最終輸出的結(jié)果如下：
mlst輸出結(jié)果
參考
mlst軟件源地址：https://github.com/tseemann/mlst
所用菌株：
GCF_001660565.1
GCF_001679985.1
GCF_001682305.2
