Document the relationship between ont-guppy-duplex-pipeline and duplex_tools about duplex-tools HOT 3 OPEN

Sorry, my mistake - I see ont-guppy-duplex-pipeline does also incorporate an alignment-based filtering step, but it does not yield the same results as this package. I get about twice the number of candidate duplex pairs. I guess I'll need to actually basecall these to see how many are false positives.

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Hi @tbooth,

The scripts in the current version in Guppy were taken from an earlier version of this repository, hence the similarities. Guppy needs updating, IIRC the major difference is the compute performance. @ollenordesjo can comment on the output differences.

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Hi @tbooth, sorry, have been on vacation, just seeing this now.

The option that mostly affects the output results is the min_qscore filter (https://github.com/nanoporetech/duplex-tools/blob/master/duplex_tools/pairs_from_summary.py#L320). Without re-running the same things through ont-guppy-duplex-pipeline and duplex_tools and checking carefully, that would be my first guess on why the number of candidate duplex pairs are different.

Depending on your requirements, you may want to set this threshold lower than the default (I would suggest including the best ~85% of reads or something similar, whereever that threshold may be for your dataset). We had some discussions about setting this threshold more adaptively, but decided that a constant threshold would keep it more reproducible on a per-read level.

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