Hey Guys
Just wondering if you guys have come across or developed any process to check for contamination in PacBio reads. By contamination what I mean is to align/blast the PacBio reads to some reference like (nt, 16s etc) to see if proportion of reads hit something not expected pointing to a possible contamination.
Since there is inherent indel errors in the PacBio data, standard blast penalizes the alignment (due to lot of possible gap introductions) which could result in reads not aligning at all.
It would be nice to know what you guys are doing with the contamination check on Pacbio long reads.
Best, -Abhi