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Bio-MLST-Check-2.1.1630910
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Multilocus sequence typing

Build Status

This application is for taking MLST databases from multiple locations and consolidating them in one place so that they can be easily used (and kept up to date). Then you can provide FASTA files and get out sequence types (ST) for a given MLST database. Two spreadsheets are outputted, one contains the allele number for each locus, and the ST (or nearest ST), the other contains the genomic sequence for each allele.
If more than 1 allele gives 100% identity for a locus, the contaminated flag is set. Optionally you can output a concatenated sequence in FASTA format, which you can then use with tree building programs. New, unseen alleles are saved in FASTA format, with 1 per file, for submission to back to MLST databases.

Usage

The MLST databases must be downloaded first. This is something you would only do every now and again. You need to set the $MLST_DATABASES environment variable first to a location where you want to save your databases. If you use Docker, you can skip this step as the databases are bundled with the container.

Usage: download_mlst_databases [options]
   -c STR Config file containing details of MLST databases from pubMLST
   -b STR Directory where MLST databases are stored [$MLST_DATABASES]
   -h     Print this message and exit
   -v     Print version number and exit

The get_sequence_type script allows you to calculate the ST of a FASTA file against one or more database. If you dont provide the '-s' option, then every database will be searched. If you wish to build a phylogenetic tree of then use the '-c' or '-y' options to get a single aligned FASTA/Phylip file.

Usage: The get_sequence_type [options] *.fasta

   -s STR Species of MLST database (0 or more comma separated)
   -d INT Number of threads [1]
   -c     Output a FASTA file of concatenated alleles and unknown sequences 
   -y     Output a phylip file of concatenated alleles and unknown sequences
   -o STR Output directory [.]
   -a     Print out all available MLST databases and exit
   -h     Print this message and exit
   -v     Print version number and exit

Input format

The input files must be in FASTA format.

Outputs

mlst_results.allele.csv

This is a tab separated spreadsheet containing the ST number of each input FASTA file and the corresponding allele numbers for each gene in the scheme. If one of the alleles is not contained in the database, then it will be flagged with 'U' and the 3rd column will describe it as 'Unknown'. If the combination of allele numbers has never been seen before, it will be flagged as 'Novel'. The ST column is populated with the nearest ST found. Should two diffent alleles for a single gene be found, then the allele numbers will be put into the 'Contamination' column (since there shouldnt be 2 copies of these genes). However some schemes are poorly defined so take it with a pinch of salt.

Isolate | ST |"New ST" |Contamination | aroC | dnaN | hemD | hisD | purE | sucA | thrA ------- | --- | --------|------------------|------|------|------|------|------|------|----- sample1 | ~559| Unknown | | 130 | 97 | 25 | 125 | U | 9 | 101 sample2 | 518 | | | 101 | 41 | 40 | 184 | 76 | 90 | 3 sample3 | 150 | | purE-422,purE-84 | 130 | 97 | 25 | 125 | 422 | 9 | 101 sample4 | ~150| Novel | | 130 | 95 | 25 | 125 | 422 | 9 | 101

mlst_results.genomic.csv

This spreadsheet is similar to the mlst_results.allele.csv spreadsheet, however it gives the full sequences of each allele instead of the allele number.

*unknown.fa

You can choose to output any new alleles (-c) which are not contained in the MLST database. These can then be used to feedback to the curators maintaining the MLST databases, where they can be assigned allele numbers and profiles.

concatenated_alleles.fa and concatenated_alleles.phylip

You can choose to output a multiple FASTA/Phylip alignment of all of the MLST genes concatenated together, where each sample is represented by a single sequence. This file can then be used as input to a phylogenetic tree building application (such as RAxML or FastTree) to create a phylogenetic tree (dendrogram).

#Installation Instructions are given for installing the software via Docker (can be run on all operating systems) and for Debian/Ubuntu distributions.

##Docker We have a docker container which is setup and ready to go. It includes a snapshot of the MLST databases from the day it was built. To install it:

docker pull sangerpathogens/mlst_check

To use it you would use a command such as this (substituting in your directories), where your FASTA files are assumed to be stored in /home/ubuntu/data:

docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/mlst_check get_sequence_type -s "Clostridium difficile" /data/*.fa

Your results will then be in the /home/ubuntu/data directory (or whatever you have called it).

##Debian/Ubuntu If you run Debian or Ubuntu it should be straightforward to install the software. Run:

apt-get update -qq
apt-get install -y ncbi-blast+ cpanminus gcc autoconf make libxml2-dev zlib1g zlib1g-dev libmodule-install-perl
cpanm -f Bio::MLST::Check

Then you need to set a directory where you would like to store the MLST databases.

export MLST_DATABASES=/path/to/where_you_want_to_store_the_databases

Download the latest copy of the databases (run it once per month)

download_mlst_databases

Now you can use the script. For example,find the sequence types for all fasta files in your current directory:

get_sequence_type -s "Clostridium difficile" *.fa

#Reporting bugs and getting support For any queries, please file an Issue on GitHub or failing that contact path-help@sanger.ac.uk

#Contribute to the software If you wish to fix a bug or add new features to the software we welcome Pull Requests. Please fork the repo, make the change, then submit a Pull Request with details about what the change is and what it fixes/adds.