FastMLST

A multi-core Multilocus Sequence Typing tool coupled with allele concatenation.

Introduction

FastMLST is a high speed standalone script wrote in Python3, which takes assemblies in FASTA format (gzipped is also allowed) and determines its ST according to MLST schemes defined in PubMLST. The main advantage over other ST determination programs is that FastMLST allows the generation of a FASTA file containing the concatenated alleles for all analyzed genomes ready to be aligned and used in phylogenetic inference.

You can read a complete guide to MLST analysis in our Wiki.

Installation

You can install FastMLST using either Conda or pip. If you want the most up-to-date version, you can install it directly from GitHub using pip.

Using Conda

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install fastmlst

Using pip for the latest version

To install the latest version directly from GitHub, use the following command:

pip install git+https://github.com/EnzoAndree/FastMLST.git

Dependencies

It is expected that all dependencies will be resolved when using conda for installation.

• Python > 3
• Biopython
• tqdm
• pandas
• NCBI BLAST+

Quick Start

$ fastmlst cdiff_refferences/RT078_CDM120.fasta
RT078_CDM120.fasta,cdifficile,11,adk(5),atpA(8),dxr(5),glyA(11),recA(9),sodA(11),tpi(8),mlst_clade(5.0)

$ fastmlst cdiff_refferences/RT078_CDM120.fasta.gz
RT078_CDM120.fasta.gz,cdifficile,11,adk(5),atpA(8),dxr(5),glyA(11),recA(9),sodA(11),tpi(8),mlst_clade(5.0)

$ fastmlst cdiff_refferences/*.fasta
RT001_BI9.fasta,cdifficile,3,adk(1),atpA(1),dxr(2),glyA(1),recA(1),sodA(1),tpi(1),mlst_clade(1.0)
RT001_Liv24.fasta,cdifficile,3,adk(1),atpA(1),dxr(2),glyA(1),recA(1),sodA(1),tpi(1),mlst_clade(1.0)
RT002_TL178.fasta,cdifficile,8,adk(1),atpA(1),dxr(2),glyA(6),recA(1),sodA(5),tpi(1),mlst_clade(1.0)
RT012_CD630_chr_V12.fasta,cdifficile,54,adk(1),atpA(4),dxr(7),glyA(1),recA(1),sodA(3),tpi(3),mlst_clade(1.0)
RT014_TL176_v3.fasta,cdifficile,13,adk(1),atpA(1),dxr(6),glyA(1),recA(5),sodA(3),tpi(1),mlst_clade(1.0)
RT015_TL174.fasta,cdifficile,44,adk(2),atpA(5),dxr(2),glyA(1),recA(1),sodA(3),tpi(1),mlst_clade(1.0)
RT017_CF5.fasta,cdifficile,86,adk(3),atpA(7),dxr(3),glyA(8),recA(6),sodA(19),tpi(11),mlst_clade(4.0)
RT017_M68.fasta,cdifficile,37,adk(3),atpA(7),dxr(3),glyA(8),recA(6),sodA(9),tpi(11),mlst_clade(4.0)
RT023_CD305.fasta,cdifficile,791,adk(65),atpA(1),dxr(4),glyA(7),recA(2),sodA(8),tpi(7),mlst_clade(nan)
RT027_CD196.fasta,cdifficile,1,adk(1),atpA(1),dxr(1),glyA(10),recA(1),sodA(3),tpi(5),mlst_clade(2.0)
RT027_R20291_July2013.fasta,cdifficile,1,adk(1),atpA(1),dxr(1),glyA(10),recA(1),sodA(3),tpi(5),mlst_clade(2.0)
RT078_CDM120.fasta,cdifficile,11,adk(5),atpA(8),dxr(5),glyA(11),recA(9),sodA(11),tpi(8),mlst_clade(5.0)
RT106_Liv22.fasta,cdifficile,42,adk(1),atpA(1),dxr(2),glyA(1),recA(1),sodA(7),tpi(1),mlst_clade(1.0)

Usage

FastMLST uses as input a assembly in FASTA format. Optionally it can be compressed with gzip or bzip2.

$ fastmlst cdiff_refferences/RT078_CDM120.fasta
RT078_CDM120.fasta,cdifficile,11,adk(5),atpA(8),dxr(5),glyA(11),recA(9),sodA(11),tpi(8),mlst_clade(5.0)

The output is a comma separated file (csv) by default, but it can be modified using the -s option.

$ fastmlst -s '\t' cdiff_refferences/RT078_CDM120.fasta
RT078_CDM120.fasta      cdifficile      11      adk(5)  atpA(8) dxr(5)  glyA(11)        recA(9) sodA(11)        tpi(8)  mlst_clade(5.0)

There are two options for saving the result in a text file:

$ fastmlst -to mlst.csv cdiff_refferences/RT078_CDM120.fasta
$ fastmlst cdiff_refferences/RT078_CDM120.fasta > mlst.csv

Both options generate the mlst.csv file containing the FastMLST result.

FastMLST is able to generate a file in FASTA format with the alleles concatenated in the same way as they are in PubMLST. If any genome is not found in this result, it means that (1) Allele contain Ns, (2) alleles missing or (3) contamination (multiple alleles for one genome). Optionally the name could be modified with -fo option:

$ fastmlst cdiff_refferences/RT078_CDM120.fasta

FastMLST will try to use all available cores. It can be modified with -t option:

$ fastmlst -t 2 cdiff_refferences/RT078_CDM120.fasta 

You also can specify to FastMLST the scheme name using the --scheme option, this is particularly useful when there is more than one scheme per species. If you use this option, it will generate a table with a new format (available since version 0.0.10) which is easier to use in other programs like phyloviz.

$ fastmlst --scheme cdifficile cdiff_refferences/RT078_CDM120.fasta
Genome,Scheme,ST,adk,atpA,dxr,glyA,recA,sodA,tpi,mlst_clade
RT078_CDM120.fasta,cdifficile,11,5,8,5,11,9,11,8,5.0

If you want the old format just add the option --legacy:

$ fastmlst --legacy --scheme cdifficile cdiff_refferences/RT078_CDM120.fasta
RT078_CDM120.fasta,cdifficile,11,adk(5),atpA(8),dxr(5),glyA(11),recA(9),sodA(11),tpi(8),mlst_clade(5.0)

A list of schemes supported is displayed with the option --scheme-list in the following format (n) code_name: Full species name

Hint: You must use just the code_name in the --scheme option.

$ fastmlst --scheme-list
There are 153 schemes (A round of applause to @keithajolley! (Jolley, et al., 2018)):

(1) achromobacter: Achromobacter spp.
(2) abaumannii#1: Acinetobacter baumannii#1
(3) abaumannii#2: Acinetobacter baumannii#2
(n) (...)
(151) xfastidiosa: Xylella fastidiosa
(152) ypseudotuberculosis: Yersinia pseudotuberculosis
(153) yruckeri: Yersinia ruckeri

A new option in version v0.0.14 is the possibility to obtain the alleles divided into individual FASTA files (one for each allele in the scheme), ready to be used in other programs such as MLSTest.

$ fastmlst --scheme cdifficile cdiff_refferences/*.fasta --splited-output splited_mlst
Genome,Scheme,ST,adk,atpA,dxr,glyA,recA,sodA,tpi,mlst_clade
RT001_BI9.fasta,cdifficile,3,1,1,2,1,1,1,1,1.0
RT001_Liv24.fasta,cdifficile,3,1,1,2,1,1,1,1,1.0
RT002_TL178.fasta,cdifficile,8,1,1,2,6,1,5,1,1.0
RT012_CD630_chr_V12.fasta,cdifficile,54,1,4,7,1,1,3,3,1.0
RT014_TL176_v3.fasta,cdifficile,13,1,1,6,1,5,3,1,1.0
RT015_TL174.fasta,cdifficile,44,2,5,2,1,1,3,1,1.0
RT017_CF5.fasta,cdifficile,86,3,7,3,8,6,19,11,4.0
RT017_M68.fasta,cdifficile,37,3,7,3,8,6,9,11,4.0
RT023_CD305.fasta,cdifficile,791,65,1,4,7,2,8,7,
RT027_CD196.fasta,cdifficile,1,1,1,1,10,1,3,5,2.0
RT027_R20291_July2013.fasta,cdifficile,1,1,1,1,10,1,3,5,2.0
RT078_CDM120.fasta,cdifficile,11,5,8,5,11,9,11,8,5.0
RT106_Liv22.fasta,cdifficile,42,1,1,2,1,1,7,1,1.0

$ ls splited_mlst/
adk.fasta  atpA.fasta  dxr.fasta  glyA.fasta  recA.fasta  sodA.fasta  tpi.fasta
$ cat splited_mlst/adk.fasta
>RT001_BI9.fasta adk
CATATATCAACAGGAGATATATTCAGAAAGAATATAAAAGAGGGAACAGAACTTGGAAAA
AAAGCTAAAGAATACATGGACCAAGGTTTATTAGTACCAGATGAGTTAACTGTAGGTTTA
GTTACTGATAGAATATCTCAAGAAGATTGTAAAAATGGATTTATGTTAGATGGATTTCCA
AGAAATGTAGCACAAGGAGAACATTTAGATATCTTCTTAAAAAATGCTGGTATATCACTA
GATAAAGTTGTCAATATTGAAGTTGATAAGAGTATATTAGTGTCTAGAGCAGTTGGTAGA
AGAATATGTAAGTCTTGTGGAGCTACTTACCATGTTGAGTTTAATCCTCCTAAAGTAGAA
GGTGTATGTGATGTATGCCAAGGAGAATTATATCAAAGAGCTGATGATAATGAAGAAACT
GTATCTAAGAGAATACAAGTTTATCTAGATGAAACTAAGCCTTTAGTAGATTATTATAGC
AAACAAGGTATAATAGCAGAT
...
>RT106_Liv22.fasta adk
CATATATCAACAGGAGATATATTCAGAAAGAATATAAAAGAGGGAACAGAACTTGGAAAA
AAAGCTAAAGAATACATGGACCAAGGTTTATTAGTACCAGATGAGTTAACTGTAGGTTTA
GTTACTGATAGAATATCTCAAGAAGATTGTAAAAATGGATTTATGTTAGATGGATTTCCA
AGAAATGTAGCACAAGGAGAACATTTAGATATCTTCTTAAAAAATGCTGGTATATCACTA
GATAAAGTTGTCAATATTGAAGTTGATAAGAGTATATTAGTGTCTAGAGCAGTTGGTAGA
AGAATATGTAAGTCTTGTGGAGCTACTTACCATGTTGAGTTTAATCCTCCTAAAGTAGAA
GGTGTATGTGATGTATGCCAAGGAGAATTATATCAAAGAGCTGATGATAATGAAGAAACT
GTATCTAAGAGAATACAAGTTTATCTAGATGAAACTAAGCCTTTAGTAGATTATTATAGC
AAACAAGGTATAATAGCAGAT

Custom MLST Database Location

FastMLST now supports configuring a custom location for the PubMLST database. By default, the tool uses a cache directory at ~/.cache/fastmlst/pubmlst. However, if you prefer to store the database in an alternate location (for example, on a high-performance drive or in a centralized directory), you can override this default path using the --db_path command-line argument.

How It Works

When the --db_path option is provided, FastMLST calls a helper function (set_pathdb) that:

• Overrides the default database path: The internal global pathdb variable is updated to use your specified path.
• Ensures the custom directory exists: The directory is automatically created if it does not exist.
• Uses the custom path for all subsequent operations: All processes (such as fetching, updating, or reading database files) use the new path.

Usage Example

To run FastMLST with a custom MLST database directory, simply use the --db_path option:

$ fastmlst --db_path /path/to/your/custom/db [other-options] genomes...

For instance, if you want the MLST database to reside in /data/fastmlst_db, run:

$ fastmlst --db_path /data/fastmlst_db cdiff_refferences/RT078_CDM120.fasta

When to Use This Feature

• Optimizing I/O Performance: Place the database on a disk wi