Generic typing tool from amplicons and/or in silico PCR
There are numerous genotyping systems for microbes, but they all have something in common: they identify small pieces of genome sequence that are useful in some way, and use combinations of these sequences to assign a "type", usually a single number. The classic example of this being MLST.
Traditionally in the wet lab these sequences would be determined by using PCR primers followed by Sanger capillary sequencing. In the new world of WGS, we have sequence reads (FASTQ) or assembled contigs (FASTA). With contigs, we can either use in silico PCR, or identify the amplicon directly, with BLAST for example.
Once we have identified all relevant amplicons, the amplicon (allele) combinations are converted into a genotype using a "profile table" like this:
TYPE AMP_1 AMP_2 AMP_3
1 1 1 1
2 2 1 1
3 3 1 2
...
324 23 178 76
% amplikate --version
amplikate 0.1.2
conda install -c conda-forge -c bioconda -c defaults amplikate # COMING SOON
Install HomeBrew (Mac OS X) or LinuxBrew (Linux).
brew install brewsci/bio/amplikate # COMING SOON
This will install the latest version direct from Github.
You'll need to add the amplikate bin directory to your $PATH,
and also ensure all the dependencies are installed.
cd $HOME
git clone https://github.com/tseemann/amplikate.git
$HOME/amplikate/bin/amplikate --help
perl>= 5.26
amplikate is free software, released under the GPL 3.0.
Please submit suggestions and bug reports to the Issue Tracker