Hi,
I want to find pan genome in bacteria, which include subsequent analysis of core, dispensable and singleton genome of bacteria. Which software is recommended to manage about 50-60 genomes?
Hi,
I want to find pan genome in bacteria, which include subsequent analysis of core, dispensable and singleton genome of bacteria. Which software is recommended to manage about 50-60 genomes?
Before trying anything and running into trouble, I'd suggest you read comparisons between the available programs, like these recent papers:
I use both Spine/AGEnt (DNA- based) and Roary (protein- based). Roary is especially useful if you're annotating novel genomes with Prokka, as it takes the Prokka's GFF output directly as input, without any conversions in between.
I found get_homologues quite powerful and useful.
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis.
Contreras-Moreira B1, Vinuesa P.
I think PGAP is one of your option. But I'm not sure whether it will be working standalone PC though.
Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29. PGAP: pan-genomes analysis pipeline. Zhao Y1, Wu J, Yang J, Sun S, Xiao J, Yu J.
What is your operating system?