Question: pipelines for pan-genome analysis
0
gravatar for akhilvbioinfo
5.3 years ago by
akhilvbioinfo150
India, chennai
akhilvbioinfo150 wrote:

I have bacterial genome and  which pipeline is best  for pan-genome analysis ? 

genome • 2.7k views
ADD COMMENTlink modified 3.3 years ago by Optimist100 • written 5.3 years ago by akhilvbioinfo150

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.

ADD REPLYlink written 5.1 years ago by Nari880
1
gravatar for Optimist
3.3 years ago by
Optimist100
Optimist100 wrote:

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

ADD COMMENTlink written 3.3 years ago by Optimist100

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.

ADD REPLYlink written 2.5 years ago by ambrinaakbar10
1

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

ADD REPLYlink written 2.5 years ago by Optimist100
0
gravatar for dago
5.3 years ago by
dago2.6k
Germany
dago2.6k wrote:

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

I found this program really good!

ADD COMMENTlink written 5.3 years ago by dago2.6k
0
gravatar for Nari
5.1 years ago by
Nari880
United States
Nari880 wrote:

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

sourceforge link

ADD COMMENTlink modified 12 months ago by _r_am31k • written 5.1 years ago by Nari880
0
gravatar for Nari
5.1 years ago by
Nari880
United States
Nari880 wrote:

This is the list of all tools.

refer to this page.

ADD COMMENTlink written 5.1 years ago by Nari880
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