Question: SNP analysis between two bacterial genomes
1
gravatar for namgyalwangstuklama
3.0 years ago by
namgyalwangstuklama10 wrote:

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

snp • 2.3k views
ADD COMMENTlink modified 3.0 years ago by Brian Bushnell17k • written 3.0 years ago by namgyalwangstuklama10

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

ADD REPLYlink written 18 months ago by genebow160

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

ADD REPLYlink written 18 months ago by WouterDeCoster43k
1
gravatar for Israel Barrantes
3.0 years ago by
Germany
Israel Barrantes790 wrote:

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 COMMENTlink written 3.0 years ago by Israel Barrantes790
0
gravatar for Brian Bushnell
3.0 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

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 COMMENTlink modified 3.0 years ago • written 3.0 years ago by Brian Bushnell17k
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