Joel Boyd
Hi Siavash, First, the SEPP, TIPP, UPP and HIPPI suite look very interesting and I'm excited to try them out - SEPP in particular I'm wondering if it would it...
…ee. This update also includes a Taxonomy module which will eventually be implemented across GraftM. Currently taxonomy is read in at multiple places in the GraftM code, making it less...
Hey here is the .jplace file patch. It is synced with the slash error branch so please have a look at that one first (https://github.com/geronimp/graftM/pull/171) just so you're aware of...
Patch to the /2 /1 ending error. I also added another test which tests for another bug I found when trying to merge reads with /2 /1 endings. Some changes...
Try here
Can now update CONTENTS file of GraftM package with a little more ease.
The actual assignment of classification is never explicitly tested
HMM-based searching is biased against archaea due to the over-representation of bacteria in the models. GraftM create needs to have some way of producing HMMs for sub-groups within gene families...