This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Do the BLAST and BLAST+ algorithms ignore the NNs in scaffolds/genomes or not?

Hi, I am new to NGS/ genome assembly field. I am given data and assembly (done by someone else) to evaluate if it is correct and if not, do the assembly myself. To check the given draft assembly, I mapped the largest scaffold of the existing reference genome (about 4Mb), using it as query to our draft assembly with blast+ and found that the query scaffold maps to 195 different scaffolds of the draft assembly. 1. I think this means that the assembly is highly fragmented?

The person is justifying this by saying that it is due to the presence of several gaps (Ns) in the query scaffold. Can someone please shed some light on this matter?

blast algorithm
• 2,354 views • link
written by mirza mirza

Not answering your question, but instead recommending QUAST for assembly quality evaluation.

• 0 views • link
written by 5heikki 5heikki

Thanks but I know about Quast and have all the intentions to use it but this is something very basic which generally doesn't come to mind. So, I want to clarify and what better platform than Biostar.

• 0 views • link
written by mirza mirza

Please use ADD REPLY/ADD COMMENT to respond to existing posts to keep threads logically organized.

• 0 views • link
written by GenoMax GenoMax

I apologize. I realized after sending it.

• 0 views • link
written by mirza mirza

No need to apologize. Just wanted to make you aware in case you did not know.

• 0 views • link
written by GenoMax GenoMax

0 answers

No answers yet.

Log in to answer this question.

More posts like this