How do I remove certain reads from my raw sequencing data using BLAST?

Question

[yh1126]

I want to remove mitogenomes and other artefactual contaminations that match those on database on BLASTn. How can I remove them?

Answer 1

[jv]

It's not BLAST, but BBDuk is a good tool for removing reads that map to a set of user defined sequences.

https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/

[GenoMax]

bbduk.sh in filter mode (which is the default). You will need to provide a set of sequences you want to check against.

If you want to collect the filtered sequences into bins then using bbsplit.sh would be appropriate.

In this case if you don't know what the contamination is from then other strategies may need to be deployed.