Question

Tool:BPGA - Bacterial Pan Genome Analysis pipeline

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8.6 years ago

bpgatool ▴ 80

BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core, MLST as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc..

BPGA Sourceforge Page.
BPGA HomePage.

It was recently published in Scientific Reports.

Any suggestions for further improving the tool are welcome.

sequence genome comparative-genomics bacteria • 6.3k views

ADD COMMENT • link updated 17 months ago by Ram 44k • written 8.6 years ago by bpgatool ▴ 80

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does it give us the name of all those genes which are core genes?

ADD REPLY • link 4.9 years ago by nosheenqureshi1994 • 0

score 1 · Answer 1 · 2017-11-16

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7.1 years ago

ambrinaakbar ▴ 10

Hi, would this software helpful to find out variants in whole MLST database?

ADD COMMENT • link 7.1 years ago by ambrinaakbar ▴ 10

score 0 · Answer 2 · 2018-05-30

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6.5 years ago

Dattatray Mongad ▴ 380

How can I update COG and KEGG data for using it with BPGA?

ADD COMMENT • link 6.5 years ago by Dattatray Mongad ▴ 380

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COG is 2003 database with update on 2014. As of my knowledge it has not been updated since. So BPGA uses this only. You can use KAAS to re-annotate the fasta file.

ADD REPLY • link 6.5 years ago by Naren ▴ 1000