Removing contaminations from PacBio reads

Question

[Ric]

Hi I have PacBio RS II and Sequal reads. I am looking for a tool which removes common contaminations and allow also to provide fasta files with chloroplast and mitochondrial genomes and it would remove these genomes from the reads too.

Thank you in advance.

[GenoMax]

If you know what contaminant genomes are present then you could see if bbsplit.sh from BBMap suite may work. Otherwise use mapPacBio.sh (again from BBMap) to get the reads you want (assuming you have a reference) and leave the rest behind.

[Rox]

Hi Ric, did you managed to solve your issue using Genomax answer ? I'm still stuck with this question, because I don't now yet all organism that contaminated my assembly. Any others suggestions ? I was thinking about blasting maybe a sequence highly specific to bacteria, which is shared among bacteria (maybe following the busco criterias) and then remove all contigs that contains theses sequences... Does that sound good, or is it a bit harsh ?