Hi all,
We have observed some SNP sites and Indels by aligning our contigs to the reference genome. We want to distinguish real variants from those due to sequencing errors.
I have found several tools for variants detection but all of them work with the raw reads. I think a lot of information would be lost if assembled contigs used for this task... However, we performed a de novo assembly of the 454 reads due to the design of this specific project. It would be great if we could estimate the "confidence" of the variants we found after assembly. Is there any variant validation method working with contigs?
Or can I verify this by an independent analysis performed on the raw reads? I am afraid the variants identified before and after assembly would be somewhat inconsistent...
And, is there significant improvement if the variants are identified by using raw reads, rather than assembled contigs?
Thanks in advance.
We have observed some SNP sites and Indels by aligning our contigs to the reference genome. We want to distinguish real variants from those due to sequencing errors.
I have found several tools for variants detection but all of them work with the raw reads. I think a lot of information would be lost if assembled contigs used for this task... However, we performed a de novo assembly of the 454 reads due to the design of this specific project. It would be great if we could estimate the "confidence" of the variants we found after assembly. Is there any variant validation method working with contigs?
Or can I verify this by an independent analysis performed on the raw reads? I am afraid the variants identified before and after assembly would be somewhat inconsistent...
And, is there significant improvement if the variants are identified by using raw reads, rather than assembled contigs?
Thanks in advance.
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