1. Peter Kruczkiewicz Avatar Peter Kruczkiewicz
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MicrobialInSilicoTyper

MicrobialInSilicoTyper (MIST) allows you to perform a battery of genetic fingerprinting methods on whole genome sequences (WGS) to produce in silico typing results. MIST allows you to add existing typing methods as well as novel methods into an analysis package for your organism of interest.

From running MIST.exe with -h or without any command-line arguments:

MIST argument exception: No multifasta input(s) specified. MIST could not run.
Try `MIST --help' for more information.
Usage: MIST [OPTIONS]+ [Multifasta files]
Generate in silico typing results for an organism using WGS data in multifasta format.

Options:
  -t, --test=VALUE           Test info file. Typing test to perform.
  -a, --allele-dir=VALUE     Alleles directory
  -b, --beautify             Make your JSON beautiful!
  -o, --results-out=VALUE    Output filename for results. Default (-)/stdout.
  -w, --wordsize=VALUE       BLAST word size for PCR based tests. Default=7
  -T, --temp-dir=VALUE       Directory in which to save temporary data (e.g. 
                               BLAST output and BLAST databases)
  -c, --cores=VALUE          Number of cores to allow MIST to utilize 
                               (default=as many as the system is willing to 
                               offer)
  -j, --json-out=VALUE       json output filename. Default (-)/stdout.
  -A, --output-allele-sequences
                             Output the allele sequences in the JSON output 
                               under TestMarkers
  -h, --help                 show this message and exit

Getting Started

Windows

Linux

Compiling from source on Linux

You'll need to install Mono specifically the following packages:

  • mono-xbuild
  • mono-devel
  • mono-runtime
  • mono-dmcs

Ubuntu-like Linux:

#!bash
sudo apt-get install mono-xbuild mono-devel mono-dmcs mono-runtime

Compiling:

#!bash
git clone https://peterk87@bitbucket.org/peterk87/mist.git
cd mist
xbuild MIST.sln /p:Configuration=Release
echo "MIST.exe should be in bin/Release/ assuming no compile errors"

Running MIST on Linux

Template command-line:

#!bash
mono /path/to/bin/Release/MIST.exe -t MIST_markers_file.markers -a alleles_dir/ -c 1 -j MIST-output.json genome.fasta
Running MIST in parallel using GNU parallel

Install GNU parallel if it's not installed, e.g.

sudo apt-get install parallel

An example command

#!bash
parallel mono /path/to/bin/Release/MIST.exe -T /tmp/mist_tmp -t MIST_markers_file.markers -a alleles_dir/ -c 1 -j MIST_test-{}.json {} ::: genomes/*.fasta

Issues?

If errors are encountered please ensure .NET 4.0+/Mono 2.10+ is installed and that BLAST+ is installed and can be called through the cmd-line.

Updated