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Sequence Typing

The mlst module uses mlst scan assemblies and determine the sequence type. It makes use of PubMLST schemes and by default automatically scans each schema. To specify a specific scheme to scan, you can provide it with --scheme.

Output Overview

Below is the default output structure for the mlst step in Bactopia. Where possible the file descriptions below were modified from a tools description.

│   └── tools
│       └── mlst
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf-mlst.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── mlst-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── mlst-concat
        │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── mlst.tsv
        └── nf-reports
            ├── mlst-report.html
            ├── mlst-timeline.html
            └── mlst-trace.txt


Merged Results

Below are results that are concatenated into a single file.

Filename Description
mlst.tsv A merged TSV file with mlst results from all samples


Below is a description of the per-sample results from mlst.

Filename Description
<SAMPLE_NAME>.tsv A tab-delimited file with mlst result, see mlst - Usage for more details

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.


Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension Description
.begin An empty file used to designate the process started
.err Contains STDERR outputs from the process
.log Contains both STDERR and STDOUT outputs from the process
.out Contains STDOUT outputs from the process
.run The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh The script executed by bash for the process
.trace The Nextflow Trace report for the process
versions.yml A YAML formatted file with program versions



Parameter Description
--scheme Don't autodetect, force this scheme on all inputs
Type: string
--minid Minimum DNA percent identity of full allelle to consider 'similar'
Type: integer, Default: 95
--mincov Minimum DNA percent coverage to report partial allele at all
Type: integer, Default: 10
--minscore Minumum score out of 100 to match a scheme
Type: integer, Default: 50
--nopath Strip filename paths from FILE column
Type: boolean


If you use Bactopia and mlst in your analysis, please cite the following.