scapper

Rapid whole genome SNP alignments from multiple draft genomes

Introduction

Core genome SNP alignments are useful, but spatial information is lost because converved columns are removed, and non-core regions are excluded. Scapper is a fast way to take a bunch of genomes (closed or draft contigs) and produce a whole genome alignment.

Dependencies

• MUMmer >= 3.23
• BioPerl >= 1.60
• TrimAL >= 1.4

Installation

% cd $HOME
% git clone https://github.com/tseemann/scapper.git
% $HOME/scapper/bin/scapper -h

Usage

% ls
reference.fa draft1.fa draft2.fa draft3.fa
% scapper --output outname reference.fa draft1.fa draft2.fa draft3.fa
% ls outname.*
outname.aln  outname.nogaps.aln  outname.core.aln  outname.nogaps.aln

Output files

• output.aln has the global alignment with conserved columns and gaps
• output.nogaps.aln has the global alignment with all gap columns removed
• output.core.aln has the global alignment with conserved columns removed
• output.nogaps.core.aln has the global alignment with gaps and conserved columns removed (aka "core SNPs")

Caveats

• Everything is relative to the first genome supplied