pipelines for pan-genome analysis

Question

[Eva_Maria]

I have bacterial genome. Which pipeline is best for pan-genome analysis?

[Naren]

What are your specific requirements. What else do you want to study along with pan genome profiles. Different tools provide different downstream analyses like phylogeny, COG KEGG assignments.

Answer 1

[Optimist]

Hi Akhil,

i'm also working on the Pan genome analysis of few bacterial Genomes.

I have started to use BPGA for my analysis.

It's pretty good and user friendly. It is compatible with Linux and windows as well

You need the protein.faa files as the input to the pipeline. The output has three different folders named Results, Sequences, Supporting Files.

It gives the data related to Core and Pan plots, histograms, Functional analysis like KEGG and COG pathways etc.

Feel free to ping me regarding this. Lets learn together

Regards Optimist

[ambrinaakbar]

Hi, Optimist

I am also trying to work on BPGA but I am facing problem and have error Error: Required file: INPUT_all.faa/.ffn is missing!!!

           Probably you have not used Option 1 yet!

Kindly help me to sort out. Thanking you.

[Optimist]

Hello Anbrinaakbar,

INPUT_all.faa is generated by BPGA upon successful execution of Option 1. INPUT PREPARATION FOR CLUSTERING.

This clusters all the genome sequences under study for all the downstream analysis.

You may have to re run the program using option 1.

regards Optimist

Answer 2

[dago]

Look here..http://omictools.com/get-homologues-s6106.html

I found this program really good!

Answer 3

[Naren]

Try BPGA - A tool for fast pan-genome analysis of microbes.

sourceforge link

Answer 4

[Naren]

This is the list of all tools.

refer to this page.