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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.
- For the GUI version of MIST (currently only supported under Windows):
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
- Windows XP or higher supported.
- .NET Framework 4.0+ on Windows
Linux
- Mono 2.10+ on Linux
- BLAST+ installed with ability to call 'blastn', 'makeblastdb', etc from the command-line
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.
- If errors are still encountered, please file an issue on Bitbucket
- For further information please consult the wikis
- For the GUI version of MIST (Windows-only at the moment)
Updated