Chris Fields

When I read the documentation re: Magic Blast it seems like the primary use case is read alignment against a single reference genome, and not against a larger database (e.g....

@biocyberman my question was primarily b/c I haven't seen this used very often, particularly for this use case. For instance we've actually had very good luck with DIAMOND for this...

This worked for me fixing a parsing issue on my MacBook Pro M1.

Just a note that I am also seeing something that is likely due to this issue. I recently did a (rough) comparison of Illumina V4 and PacBio full length 16S...

@hhollandmoritz did the recommendation mentioned above by @benjjneb (https://github.com/benjjneb/dada2/issues/791#issuecomment-502256869) act as a reasonable workaround for binning? **EDIT**: I should mention I work at the same biotech center that produced the...

@hhollandmoritz ah missed that in your reply, apologies! We'll implement a binning flag in our workflow for these instances, fingers crossed!

For anyone following this: we (@jgrembi, myself, and our seq core) received an update from Illumina. It appears the binning changed in the NVCS v1.1 update to 2, 11, 25...

Speaking of... @benjjneb should this ticket stayed closed or be re-opened?

To add a little to this, here is a small test run using default nbases but employing the Q40 adjustment @benjjneb mentioned. Normal (no correction):  With Q40...

@benjjneb we do have some mock Zymo NovaSeq, but it is V3-V4; I assume you preferably want V4?