Pan- and core- genome in bacteria

Question: Pan- and core- genome in bacteria

5.1 years ago by

CikLa • 90

Malaysia

CikLa • 90 wrote:

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?

bacteria pangenome • 2.8k views

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modified 4.6 years ago by yeonbum Kim • 0 • written 5.1 years ago by CikLa • 90

What is your operating system?

ADD REPLY • link written 5.1 years ago by Nari • 880

5.1 years ago by

Israel Barrantes • 790

Germany

Israel Barrantes • 790 wrote:

Before trying anything and running into trouble, I'd suggest you read comparisons between the available programs, like these recent papers:

Vernikos, G., Medini, D., Riley, D. R., & Tettelin, H. (2014). Ten years of pan-genome analyses. Current Opinion in Microbiology, 23C, 148–154. doi:10.1016/j.mib.2014.11.016
Xiao, J., Zhang, Z., Wu, J., & Yu, J. (2015). A Brief Review of Software Tools for Pangenomics. Genomics, Proteomics & Bioinformatics, 13(1), 73–6. doi:10.1016/j.gpb.2015.01.007

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.

ADD COMMENT • link modified 5.1 years ago • written 5.1 years ago by Israel Barrantes • 790

5.1 years ago by

Nari • 880

United States

Nari • 880 wrote:

I have developed one. Try BPGA.

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5.1 years ago by

HG • 1.1k

Germany

HG • 1.1k wrote:

try https://github.com/jasonsahl/LS-BSR

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5.1 years ago by

dago • 2.6k

Germany

dago • 2.6k wrote:

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.

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4.6 years ago by

yeonbum Kim • 0

Korea, Republic Of

yeonbum Kim • 0 wrote:

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.

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