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/
makeRun BactCore
BactCore <input.fasta> <output>And for strict cores (sites with no gaps):
BactCore --strict <input.fasta> <output.fasta>Or SNP-sites only from the strict core sites:
BactCore --strict --snps <input.fasta> <output.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