mlst这个软件顾名思义就是做mlst的，需要的只是fasta,gbk,embl文件。
安装当然还是conda
conda install -c bioconda mlst
输入
mlst -h
查看用法和参数
USAGE
% mlst --list 列出所有可以分析的细菌种属#
% mlst [options] <contigs.{fasta,gbk,embl}[.gz] 自动选择所用种属
% mlst --scheme <scheme> <contigs.{fasta,gbk,embl}[.gz]> 指定种属
参数很多，常用的如下：
--scheme 指定需要的种属，如ecoli (可用--list查看）
--legacy 传统的输出方式输出结果
--csv 输出一个csv文件，方便使用excel后续处理
--threads 分析所用线程数量
查看现在支持的细菌种属
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株大肠杆菌为例，以传统模式输出结果到csv文件：
mlst --scheme ecoli --legacy --csv *.fna > mlst.csv
最终输出的结果如下：
mlst输出结果
参考
mlst软件源地址：https://github.com/tseemann/mlst
所用菌株：
GCF_001660565.1
GCF_001679985.1
GCF_001682305.2
