seqkit amplicon only keeps one amplicon

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#191 5 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
38/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
go
Domain
bioinformatics, cli

Research direction

Start with the seqkit amplicon command and trace how it selects the largest amplicon for each primer pair. Define the behavior for retaining all valid amplicons and producing a BED file with their start and end bases in columns 2 and 3. Done means users can inspect every valid pair and choose a different amplicon.

Written by the indexing model from the issue text.

Description

enhancement

Hi,

In version 0.15.0 seqkit amplicon only keeps one amplicon (the largest) per primer pair. I don't always care about the largest amplicon.

Would it be possible to implement the feature of keeping all valid amplicons? A bed file with the start and end bases (columns 2 and 3) of all valid pairs would be fantastic. That would permit me to inspect the amplicons and keep the one I want (in my case, the smallest amplicon over a certain threshold).

Thanks

Dominant language
Go
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Forks
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