Question: PacBio raw data trimming and cleaning
gravatar for misterie
17 months ago by
misterie90 wrote:


I have done analysis of QC using FastQC for my PacBio data. I am wondering whether should I clean my data by quality criterion or minimum length of read. Those data are very poor (PacBio). Do you know any recommendation how to clean those data? For Illumina I used to use Trimmomatic, CutAdapt and TrimGalore, but I have no idea how to pre-process PacBio data. I think I should remove reads shorter than 50 bp, but if you have any other recommendation for those purposes, let me know.

pacbio cleaning qc trimming • 1.0k views
ADD COMMENTlink written 17 months ago by misterie90

Things like this usually depend on the application you want to do after cleaning. Do you want (structural) variant calling, de novo assembly,...?

ADD REPLYlink written 17 months ago by WouterDeCoster44k

I want to do de novo assembly using different pipelines. But I think I should at least trimm my data using minimum length =50bp

ADD REPLYlink written 17 months ago by misterie90

Since you are working with PacBio data I personally think it's a bit silly to use a lower bound of only 50 nucleotides. Depending on your read length distribution I would go for at least 10fold of your 50n threshold.

On the other hand most PacBio processing pipelines will already apply an internal min length filtering (mostly around few Kbp).

ADD REPLYlink written 17 months ago by lieven.sterck8.0k

Thank you. I mean mainly, that I have some samples after demultiplexing using lima and standard (default) threshold for minimum length was set to 50 Bp. I have also samples that do not require demultiplexing so there are reads that have minimum length = 1bp. I want to uniform those samples. If it could be better to change threshold to 500bp let me know which software will be appropriate.

ADD REPLYlink written 17 months ago by misterie90

it all depends on what the analyses are you want to do with the data.

eg. assembly: most assemblers will either do 'cleaning' themselves or do no quality cleaning at all

ADD REPLYlink written 17 months ago by lieven.sterck8.0k
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