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Add long-read support #101

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benjjneb opened this issue Sep 20, 2018 · 3 comments
Open

Add long-read support #101

benjjneb opened this issue Sep 20, 2018 · 3 comments

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@benjjneb
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@benjjneb benjjneb commented Sep 20, 2018

We've added support for PacBio long-read amplicon sequencing to the devel version of the R package and it seems to work quite well. Preprint: High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution.

I think it will make sense to add this as a tech-specific denoise-pacbio command in the plugin. This is similar to the denoise-pyro approach already in the plugin, with the purpose of having a dedicated command being to automatically turn on the right flags and options for PacBio data rather than relying on the user to do so. There is a downside in the repetition of much of the code between the different denoise-[technology] commands.

To be clear, this is a ways off at this point. Long-read processing won't be possible to add to the plugin until the upcoming R package release propagates to bioconda, and as of now the current R package release isn't even on bioconda yet!

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@benjjneb benjjneb commented Mar 15, 2019

This won't be in the 2019Q2 update. Tentatively targeting this for end-of-year 2019.

@colinbrislawn

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@colinbrislawn colinbrislawn commented Nov 26, 2019

What's the current status? People love those long reads! 🧬

@benjjneb

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@benjjneb benjjneb commented Nov 26, 2019

Waiting on the R package 1.12 to propagate through bioconda to Q2, as that made some important long read improvements.

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