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qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2
BSD 3-Clause "New" or "Revised" License
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adding 454/ion torrent support #76

Closed gregcaporaso closed 6 years ago

gregcaporaso commented 6 years ago

I think this is just a matter of exposing the parameters described here. I can take this one (either for 2017.10 or 2017.11), and will do some research when I work on it to figure out if it makes sense as part of an existing method or a new one or two.

benjjneb commented 6 years ago

On the dada2 side, we are updating our recommendations for IT/454. They now both should use HOMOPOLYMER_GAP_PENALTY=-1 and BAND_SIZE=32.

I think that a new command to handle both IT and 454 makes sense, something like denoise-pyro.

For 454, it would be recommended to expose the maxLen filtering parameter, as long 454 sequences were bad quality even if it didn't show up in quality scores. That doesn't matter for IT as they are all the same length.

thermokarst commented 6 years ago

This recently came up on the forum.