How can we have SAM / BAM reads to validate a de novo genome assembly?

Question

[alecloic]

Hello,

I am currently working on a de novo large genome assembly. Now I want to assess the quality of my reconstructed genome. I saw that there are several suitable programs. Some require as input reads in the format BAM / SAM. For example, there are the software:

• ALE: Assembly Likelihood Evaluator (http://www.ncbi.nlm.nih.gov/pubmed/23303509)
• CGAL: Computing Genome Assembly Likelihoods (http://blogs.biomedcentral.com/bmcblog/2013/01/29/cgal-a-new-metric-for-assessing-genome-assembly-quality/)

this are probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. they are classified as "Sequencing > De novo genome sequencing > Assembly evaluation"

But to have SAM or BAM alignment file I have to mappe my FASTQ file to the reference genome but I'm working on a de novo genome assembly. That's why I don't have a reference genome. And I do not always have an available similar genome already validated that I could use as a reference.

Some people talk to get the reads in the format BAM / SAM thanks to an alignment with my newly reconstructed genome (but therefore not validated). Do you think that this is possible? Does it help to have a correct validation? Or is it too incoherent?

Thank you

Cordially

Answer 1

[Devon Ryan]

You would normally align against your de novo assembled genome and then perform evaluation accordingly with the results.

[alecloic]

ok. thank you for your response.
I was not sure that it was very logical and software do not mention this problem.
So I'll probably do like that.