Question: Pan- and core- genome in bacteria
1
gravatar for CikLa
4.4 years ago by
CikLa90
Malaysia
CikLa90 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 • 2.6k views
ADD COMMENTlink modified 3.9 years ago by yeonbum Kim0 • written 4.4 years ago by CikLa90

What is your operating system?

ADD REPLYlink written 4.4 years ago by Nari880
6
gravatar for Israel Barrantes
4.4 years ago by
Germany
Israel Barrantes790 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 COMMENTlink modified 4.4 years ago • written 4.4 years ago by Israel Barrantes790
0
gravatar for Nari
4.4 years ago by
Nari880
United States
Nari880 wrote:

I have developed one. Try BPGA.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Nari880
0
gravatar for HG
4.4 years ago by
HG1.1k
Germany
HG1.1k wrote:

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

ADD COMMENTlink written 4.4 years ago by HG1.1k
0
gravatar for dago
4.4 years ago by
dago2.6k
Germany
dago2.6k 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.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by dago2.6k
0
gravatar for yeonbum Kim
3.9 years ago by
Korea, Republic Of
yeonbum Kim0 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.

ADD COMMENTlink written 3.9 years ago by yeonbum Kim0
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