BactCore

Extract per-site flexible (≥95%) bacterial core genome alignments from bacterial whole-genome, reference-anchored alignments, such as from read mapping.

Output includes invariant sites in the output for detection of recombinant sites with ClonalFrameML

Installation

Compile with:

git clone https://github.com/moorembioinfo/BactCore.git
cd BactCore/
make

Usage

Run BactCore, optionally specifying number of threads for extra speed

BactCore --alignment input.fasta
BactCore --proc 10 --alignment input.fasta

For the low memory implementation add:

BactCore --lowmem --alignment input.fasta

And for strict cores (sites with no gaps):

BactCore --strict --alignment input.fasta

Input

Multi-fasta whole genome alignment derived from mapping to a reference and variant calling such as from snippy, snippy-core and snippy-clean_full_aln:

snippy-core --ref ref.fa snippyoutfiles 
snippy-clean_full_aln core.full.aln > clean.full.aln

Use tools/clean_alignment.fasta if the alignment contains sites other than {ATCGN-}

Dependencies

You may need to install openMP first. There are a number of ways of doing this, I reccomend conda:

conda install -c conda-forge openmp