Interleaved Fastq input #843
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I've amended the option list for the kraken2 script with a new option interleaved and updated the usage. Interleaved allows for paired reads to be supplied in a single file and utilizes the existing hooks (-S) for doing this in classify.cc. This would directly address #670 and potentially address #669. These are very superficial changes but allow for paired reads to be passed via a pipe, a very useful but previously incompatible approach. I've tested the output versus passing the paired read files directly to Kraken2 and the results are identical.