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qiime2 / q2-vsearch

vsearch plugin for QIIME 2
BSD 3-Clause "New" or "Revised" License
6 stars 20 forks source link

Stats #62

Closed angrybee closed 4 years ago

angrybee commented 5 years ago

This branch adds the vsearch functions fastq_stats, fastq_eestats and fastq_eestats2 to the plugin.

Input are single- or paired-end fastq files. Stats are from all forward/reverse reads over all samples. The two new functions additional use the system command zcat and support multiprocessing. The output is a visualization which offers the different files for download. Data are also implemented as iframe or html table.

Missing: The unit tests. Manual diff with vsearch output was okay.

ebolyen commented 5 years ago

Hey @angrybee! Let us know when this is ready for review, I may take a quick pass shortly, but in any case, thanks for contributing!

angrybee commented 5 years ago

Hi @ebolyen ! I think you can do a first review. Functionality, basic visualization of the data, and unit tests are implemented and working.

angrybee commented 5 years ago

Thank you @thermokarst for the review and input. I added some questions and comments :)

thermokarst commented 4 years ago

Thanks @angrybee! Sorry this took so long on our end, but it is being merged now, and will be released in the upcoming 2020.5 release of QIIME 2. Thanks!