GenomeHash - A minimal-database MLST implementation

• Benjamin Goudey
• Hannah Huckstep
• Kelly Wyres
• Thomas Conway

About:

GenomeHash is a simple method for using alleleic genotyping schemes (MLST, MLVA, Phage typing etc) without the need for a reference database of alleles. This is achieved by replacing traditional numeric labels with hashes and by determining alleles for a given locus using only a minimal allele database.

Contact:

Benjamin Goudey: bgoudey@au1.ibm.com

Requirements:

• NCBI blast+ 2.2.28-2 (available as ncbi-blast+ package in Ubuntu)
• R plus the following packages
  • Biostrings
  • digest
  • mclust
  • docopt
  • stringdist
  • pbapply
  • tools
  • pacman
  • stringr

These packages will be installed by running the pre-req command

Usage:

• gh.R prereq [--install] gh.R ref --first|--medoid
• gh.R extract (--refdb ) (--output )
• gh.R hash --nchar [--st] [--header]
• gh.R -h | --help

prereq: Install R packages required to run this script. NB: does not install BLAST.

ref Extract a set of 'reference alleles' from a given allele database Input 'allele_db' and output 'ref_db' are FASTA files.

extract Extract alleles by aligning to given seedds to a set of assemblies using BLAST. Input 'contigs' and 'ref_db' and output 'alleles' are FASTA files.

hash Hash a given FASTA file of alleles.

Options:

--help -h Show these instructions.

--install List packages to be installed

--output= Output filename

--first Use first allele as seed.

--medoid Use medoid allele as seed.

--refdb= Specify the database of reference alleles to use.

--nchar= Number of characters in hash [default: 5].

--header Write out a header containing column (i.e. allele) names

--st Add a sequence type hash

Examples:

Find the reference alleles for two loci for which we observed alleles using the 'first' method

gh.R ref --first --output ./seeds_alleles.fa ./NEIS0001.txt ./NEIS0004.txt

Extract alleles from assembled contigs using derived reference alleles

gh.R extract --refdb ./seeds_alleles.fa --output ./10_6748.extract.fa ./10_6748.fas

Create five character hashes for extracted alleles and write to file

gh.R hash --nchar 5 --output ./10_6748_hashes.txt ./10_6748.extract.fa --header

License:

MIT License, see license.txt for details

Todo:

• Convert to R package while maintaining command line interface
• Add unit testing
• Improve output to allow more interpretation around confidence
• Add example data
• Add existing databases