Improvement: HiFi smrtbell adapter detection

[Sebastien-Raguideau]

Hello,

Just a quick query on adapter dectection, there is smrtbell adapter which keep poping up in our dataset, and looking blasting it at ncbi, not only ours.

I would be nice if it was possible to check its abundance even if we do remove it by default now. If not a default, the ability to ask sequali to look at custom adapter could be useful too.

Here is a threads on that adapter: https://www.seqanswers.com/forum/sequencing-technologies-companies/pacific-biosciences/36298-identify-adapter-sequences-in-pacbio-reads

Best,
Seb

[rhpvorderman]

Hi Sebastien,

custom adapters are supported. See https://sequali.readthedocs.io/en/latest/#adapter-content-module.

Sure. I can add PacBIO adapters. This was always the plan. Unfortunately I do not have the data to test... yet. Although there is probably some GIAB data available on the GIAB data indexes, so I could look that up.

I am quite sure there is no PacBIO stuff in the VecScreen as the latest additions have been Nanopore and Illumina, and before that Nanopore was not present at all .See https://github.com/rhpvorderman/sequali/pull/192/files

This was one of the things that baffled me when starting Sequali. ONT being around for 8 years, yet nobody took the time to set up proper QC practices and add adapter detection to the QC tools??? As a result the NCBI database is rife with ONT adapters as well.

There is probably some PacBIO technical documentation that I can use to add those adapters too. I will add that to my todo list. Thank you for the suggestion.

[rhpvorderman]

@Sebastien-Raguideau I could not find the technical documentation that lists the adapter sequences. Do you know where I can find it?

[Sebastien-Raguideau]

Hey sorry for late answer. I am a bit busy at the moment.

Long story short, I won't be able to help you with that.

BUT, my fellow postdoc which works way closer to lab gave me the following. This is not documentation but directly barcodes sequences and adapter.

PacBio_barcodes.zip
Sequel_16_Barcodes_v3.zip
SMRTbell_Barcoded_Adapter_Plate_3.0_bc2001-bc2096.zip

Best,
Seb

[rhpvorderman]

Thanks! I was able to find this document thanks to that information: https://www.pacb.com/wp-content/uploads/Shared-Protocol-PacBio-Barcodes-for-SMRT-Sequencing.pdf
That contains an official source.

[rhpvorderman]

Hi, I discussed it with my colleagues and currently the Pacbio knowledge here is a bit lacking. We are currently not processing many data. Since PacBIO reads are circular there are some caveats to where the adapter can be found and what that means and what not. I am not up to speed on the details.

When I add these adapters I do want the resulting plots to be informative, and I do currently not posses enough knowledge to do this in a satisfactory manner.

For the nanopore adapters for instance, I know they occur at both ends of the read, and I did very extensive comparisons to check what probe I should use in order to properly detect them. At the moment I cannot warrant such an effort for a technology we do not use as much and I am barely familiar with.

So this should be added, but it is not going to be added by me in the near future. I added a help wanted label so someone else can take a shot at it or else this will be deferred until I am a bit more comfortable with pacbio data.

EDIT: In the mean time a custom adapter file can be used.