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