John Didion

Add additional sequencers from https://docs.google.com/spreadsheets/u/3/d/1GMMfhyLK0-q8XkIo3YxlWaZA5vVMuhU1kg41g4xLkXc/htmlview?hl=en_GB

https://cutadapt.readthedocs.io/en/stable/guide.html#non-internal-5-and-3-adapters

Automatically detect adapter sequences during trim

11

This issue is to discuss the right way to implement automated adapter detection and trimming: https://github.com/jdidion/atropos/projects/1

For paired end reads, an easy way of detecting adapter sequences is to try to align read pairs, and, if there is a confident enough alignment, assume the overhangs are...

Detect command should determine whether adapters are 5' or 3'

9

The detect command is currently optimized for 3' adapter detection. It should be possible to detect which end the adapters are on by looking for where long runs of As...

Improve heuristic detection for short reads

1

When reads lengths are shorter than adapter lengths, the detect command does not do as good a job of identifying the full-length adapter sequence as FASTQC.

Clarify what the known adapters file is for (a database of adapters that can be referenced by name), and how it differs from specifying an adapter file to one of...

https://github.com/rrwick/Porechop#how-it-works