Open colinbrislawn opened 1 month ago
Hey @colinbrislawn, thanks for submitting this! People have definitely been requesting this for a while, but this will be a big undertaking. We're going to discuss this in our engineering meeting next week to see what kind of timeline makes sense for getting this implemented!
Hey @colinbrislawn circling back on this - what are some of the actions you're hoping to utilize this on downstream? Just looking for a better scope for prioritizing this - this would be easy enough to create, but we won't be able to use it with anything as it currently stands.
we won't be able to use it with anything
Yeah, we also reached this conclusion last time. Discontiguous amplicons break a lot of assumptions, so we may want to put this on hold until we have the downstream pipeline planned.
(If someone has reads like this, they should comment here what they plan to do with them!)
Gotcha! Yeah agreed, we'll put this on hold for now and see if we receive any replies (or forum posts) in the coming months. I'm going to move this to our 'approved but unscheduled' project board in the meantime!
Vsearch supports --fastq_join in which "sequences are not merged as with the fastq_mergepairs command, but simply joined with a gap."
Addition Description It would work like the existing merge-pairs (q2 plugin docs).
Current Behavior only merging is supported via overlap
Proposed Behavior Add a new semantic type for formally-paired (now concatenated!) Illumina reads Add warnings and docs about how this differs from most other methods
Questions
References Forums x-ref. 803f-1392r amplicons is 590 reads, using PE300 x-ref