cutadpt for PacBio CCS reads? · Issue #120 · marcelm/cutadapt (original) (raw)

Hi martin,
For PacBio CCS sequence, there exists several categories concatemers related adaptor and primers, as explained in cDNA_primer wiki:
https://github.com/PacificBiosciences/cDNA_primer/wiki/Artificial-concatemers%2C-PCR-chimeras%2C-and-fusion-genes.

This concatemers can be detected by:

1. using "-b" parameter of cutadapt, then deal with the "--info-file="
2. run cutadapt two times iteratively.

Because the PacBio become more and more popular, the need will grow or a specific tool should be developed.

Best,
pengcheng