Scripts and pipeline to inspect genetic variation in a series of bacterial genomes

The pipeline and scripts come with limited documentation. Please do get in touch with the author (Marco Galardini, marco@ebi.ac.uk) if you need any guidance.

A reference genome in FASTA and Genbank format is needed (deafult filenames are genome.fasta and genome.gbk). All the genomes to be analysed should be assemblies: place nucleotides fasta files in the genomes directory (genomes/*.fasta), protein fasta files in the proteomes directory (proteomes/*.faa) and gff files in the gff directory (gff/*.gff). We reccommend using prokka to generate the .faa and .gff files.

The makefile contains the various bits of the pipeline:

• make tree: core genome alignment phylogenetic tree and mash whole genome kmer distance
• make roary: pangenome
• make oma: pairwise pangenome for each strain against the reference
• make nonsyn stop: pairwise alignment of each strain agains the reference to derive SNPs

You might want to type make -n TARGET first to make sure which commands are gonna be launched

• prokka
• parsnp and harvest
• mash
• snpeff
• roary
• oma
• python (2.7+ AND 3.3+), plus the following libraries:
  • biopython
  • bcbio-gff
  • numpy
  • pandas
  • pyvcf

Copyright (C) <2015> EMBL-European Bioinformatics Institute

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

Neither the institution name nor the name pangenome_variation can be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact marco@ebi.ac.uk.

Products derived from this software may not be called pangenome_variation nor may pangenome_variation appear in their names without prior written permission of the developers. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.