/AlignRarefaction

Produce rarefaction analysis of core genome alignment-size from reference-mapped bacterial genomes

Primary LanguagePython

AlignRarefaction

Python

Generate rarefaction data from read-mapped (reference-based) bacterial whole-genome alignments. A population of bacterial genomes is input and varying population sizes sampled to assess the impact of increased number and diversity of genomes

Usage

  1. Run the main script AlignRarefaction.py referencing the path to your sample of (fasta format) genomes:

    python AlignRarefaction.py --alignment </path/to/alignment/alignmentfile>

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

Output

File Description
.csv

...

Options

Flag           Short flag Description Required Default val
--alignment -a Provide path and name of alignment file ✅
--cutoff -c Per-site percent core (integer) 95
--step -s Step for random population size sampling 10
--minpop -mp Minimum (starting) random population size 20
--iterations -itr Number of iterations per population size 100
--keepref Remove reference sequence from the alignment False