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
Compile with:
git clone https://github.com/moorembioinfo/BactCore.git
cd BactCore/
make
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
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-}
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