Can bbmap be used for mapping short contigs to reference genome?

BioInfoTools / BBMap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

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Can bbmap be used for mapping short contigs to reference genome? #34

Closed nduan1 closed 3 years ago

nduan1 commented 3 years ago

Hi,

I am trying to extract viral information from metagenome, however, 95% of the assembled viral contigs were less than 10k, so I am thinking to map the short contigs(<10k) to the reference viral genome to get more long viral contigs, can I do this by bbmap.sh?

Thank you!

Ning

epruesse commented 3 years ago

Perhaps. Try using BLAST or MUMMER's NUCMER for this.

nduan1 commented 3 years ago

Appreciate it! I will try to run it.

Best,

Ning