Question

SNP analysis between two bacterial genomes

1

Entering edit mode

7.5 years ago

namgyalwangstuklama ▴ 10

I want to perform a SNP analysis between two bacterial genomes. which tool is best for doing so? please help...

SNP • 3.8k views

ADD COMMENT • link updated 7.5 years ago by Brian Bushnell 20k • written 7.5 years ago by namgyalwangstuklama ▴ 10

0

Entering edit mode

To analyze SNP between two bacterial genomes, you may use histogram plot. You can see my programs at https://github.com/cyinbox/NGS

ADD REPLY • link 6.0 years ago by Charles Yin ▴ 180

0

Entering edit mode

Hmmm, can you elaborate how do histograms contribute to SNP identification? It is also not clear how to use the tools you linked.

ADD REPLY • link 6.0 years ago by WouterDeCoster 47k

score 1 · Answer 1 · 2017-06-01

1

Entering edit mode

7.5 years ago

Israel Barrantes ▴ 790

Use programs that have been specifically made for bacterial genomes, like Breseq (from FASTQs) or Snippy (from either FASTAs or FASTQs). In the Breseq paper you'll find the reasons why it's wrong to use programs that do not natively support haploid genomes.

ADD COMMENT • link 7.5 years ago by Israel Barrantes ▴ 790

score 0 · Answer 2 · 2017-06-01

0

Entering edit mode

7.5 years ago

Brian Bushnell 20k

BBMap's callvariants.sh natively supports haploid genomes; the default ploidy is 1. It's been used extensively tracking SNP evolution in mutant E.coli populations.

ADD COMMENT • link 7.5 years ago by Brian Bushnell 20k