making a custom reference
2
0
Entering edit mode
4.8 years ago

I have illumina short reads which I want to call SNP without using a reference genome. I want to make a consenses sequence of some selected reads and then align the other reads to it. so the basic idea is that the consensus sequence need to be act like a "dummy genome" Is there any way to do this?

genome Assembly alignment SNP • 910 views
ADD COMMENT
1
Entering edit mode
4.8 years ago
Tm ★ 1.1k

You can first denovo assemble the reads to generate consensus/contigs and then its can be used as reference to map back reads to it and call SNPs.

ADD COMMENT
1
Entering edit mode
4.8 years ago
ori ▴ 50

I think SNP is at the base position that the base in one genome (ex: genome A) is different from the base in the other genome (ex: genome B).
From your question, it seems that the reads derived from genome A and genome B are mixed in the data, and
genome A = sequences produced by some selected reads;
genome B = sequences produced by other reads.

I wonder how you extract reads of genome A from the original data, but if you can do that, I agree with toralmanvar.
You should assemble the reads derived from genome A, and you will get contigs that you called “dummy genome”.
Then you align the reads derived from genome B to the contigs of genome A, and you will detect SNPs.
I recommend that you also align the reads derived from genome A to the contigs of genome A at that time, to compare the allele frequency of two genomes.

ADD COMMENT

Login before adding your answer.

Traffic: 728 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6