Question: How can we have SAM / BAM reads to validate a de novo genome assembly?
1
gravatar for alecloic
4.4 years ago by
alecloic40
France
alecloic40 wrote:

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 asĀ  "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

ADD COMMENTlink modified 4.4 years ago by Devon Ryan91k • written 4.4 years ago by alecloic40
1
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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

ADD COMMENTlink written 4.4 years ago by Devon Ryan91k

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.

ADD REPLYlink written 4.4 years ago by alecloic40
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