ENH: add SampleData[JoinedSequencesWithQuality] as input for classify-Kraken2 #202
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Additional details and impacted files@@ Coverage Diff @@
## main #202 +/- ##
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- Coverage 98.73% 97.75% -0.99%
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Files 78 64 -14
Lines 4671 4715 +44
Branches 0 272 +272
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- Hits 4612 4609 -3
+ Misses 59 58 -1
- Partials 0 48 +48 ☔ View full report in Codecov by Sentry. |
misialq
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misialq
approved these changes
Oct 21, 2024
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Hi All,
I am currently using the metagenome distro for one of my analyses!
I was initally strugging with my percentage unclassified from
classify-kraken2. I found that joining my reads via vsearch and then runningclassify-kraken2was helping my classification significantly. So I thought It might be a good idea to expose this as an input to the method. This was super easy because it is the same directory format as SampleData[SequencesWithQuality].I have run this code change with my data and it runs with no issues. Feel free to close if there is a reason Joined sequences can't be used with Kraken2 that I haven't thought of!
This PR does rely on a PR in Demux so that these samples can be partitioned correctly.
(I originally tested this PR in 2024.5 and then I merged dev into this branch so apologizes for the funky commit history).
Let me know if you have any questions. I don't have a ton of bandwidth if this PR needs code changes but more than happy to help as much as I can!
Depends on qiime2/q2-demux#165