Add support for 'usearch_local' when using pick_otus.py with USEARCH61

[audy]

I think this would be a useful feature as --usearch_global only aligns a small percent of my reads because I haven't truncated the database to just the region that we sequenced.

We sequence using non-overlapping paired-end Illumina reads which would require me to create two databases. It's two steps fewer for me if I just use --usearch_global and a --min_query_cov close to 1.

I created an issue in biocore/brokit and am making the changes locally. I could send a pull request when I finish if the maintainers deem --usearch_local worthy of OTU picking.

[gregcaporaso]

@audy, I think we'd want some data on how this compares to --usearch_global, in terms of number of OTUs, fraction of clustered reads, how the resulting clusters affect alpha and beta diversity, etc. Note that we're in the process of trying to transition away from closed source tools, in favor of open source clustering methods (e.g., sortmerna). This isn't something that will be ready right away, but as a result we're investing less time in expanding the feature set of the usearch and uclust based OTU pickers. If you're interested in getting involved in coding/testing/benchmarking, would you be interested in getting involved in helping move toward the replacements for these OTU picking methods?

[audy]

@gregcaporaso great idea. Sortmerna looks primordial at the moment and I'm not a C++ programmer. I could help with testing/benchmarking.

[gregcaporaso]

Great, the way to go will be to connect with @ekopylova to volunteer as an early test user. @ekopylova, can you let @audy know when you're ready for test users for OTU picking with sortmerna?

[gregcaporaso]

Let's leave this as a low priority open issue for now, and if we end up dropping support in the future for the closed source OTU pickers we'll close this then.