Question: Removing contaminations from PacBio reads
2
gravatar for Ric
3.2 years ago by
Ric290
Australia
Ric290 wrote:

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.

sequencing pacbio fastq assembly • 1.5k views
ADD COMMENTlink written 3.2 years ago by Ric290

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.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by genomax84k

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 ?

ADD REPLYlink written 3.0 years ago by Rox1.2k
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