Hi everyone,
I got sequences filtered in Dada2 algorithm implemented in Qiime2, and I want to estimate SNPs in those sequences per each generated bacteria taxa and then per each sample.
Do you know if there is any good software to do that? The softwares that I am aware of do that for whole genome analysis, but in my case, I have short reads of 400bp on average.
Thanks a lot.
Hajar
Hajar El hamss
What is the purpose of the SNP analysis? I suppose you are targeting any specific taxa and for that you might want to see the SNP.
For 16S it might be tricky because the length is little bit short, but surely you can extract the sequence of the taxa you want to analyse and do a good alignment (high iteration like 1000) and do a bootstrap tree.
With the tree you can estimate the position of the taxa in the tree and with alignment you can pinpoint the SNP.
That can be the simplest solution, if you arr satisfied with the results, you could try to replicate the results with any specialized software.
Thanks a lot @ Ujjal Kumar Nath for your reply and the interesting PDF.
Thanks @ Abhijeet Singh for your suggestions, we want to estimate SNPs to study bacterial diversity within B. tabaci species in Uganda. we are targeting the top 10 taxa based on OTUs counts of the filtered reads.
Hajar El hamss
You can look on similar study done for other Bacillus species, I saw it somewhere I guess. Don't remember if it was based on illumina but you can get an idea.