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update to swarm 2 #74

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colinbrislawn opened this issue Feb 12, 2016 · 1 comment
Open

update to swarm 2 #74

colinbrislawn opened this issue Feb 12, 2016 · 1 comment

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@colinbrislawn
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The new version of swarm is out and it's pretty different from 1.2.7. This algorithm will be relevant to qiime 2 and EMP.

I'm interested in taking this one, although I'll probably need support.
@colinbrislawn
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One of the major components of this issue will be creating the feature abundance table / contingency table / .biom table of the swarm results. Remapping sequences to OTU centroids using global alignments, like in uclust, is not appropriate for swarms. I'll have to look into this more...

https://github.com/torognes/swarm/wiki/Working%20with%20several%20samples

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