benkhedher/scapper

Whole genome core alignments from multiple draft genomes

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