Chris Fields

> [@cjfields](https://github.com/cjfields) thanks so much for your input.Yes, the PacBio bioinformatician recommended filtering BAM files based on quality scores (QS30) before use. I'm currently working on this using SAMTools for...

> [@cjfields](https://github.com/cjfields) Hello, I wanted to provide an update on my progress. I began with `rq` filtering, as you recommended, using the following command: > ... > Then, I processed...

@emankhalaf that appears to be identical to the error plot you had posted in the comment earlier which (IIRC) was using the original PacBio data with default accuracy (99%, Q20)....

I agree, the histograms are nice as an option. We have also seen an issue with misplaced labels on the smudgeplot, in our case pretty extreme:

@BigFatPandar see #1892, but also note there is a newer way of treating binned quality reads @benjjneb added recently

> My understanding is that it is common for a smaller number of reads using the Kinnex approach to pass filtering, however you do filtering. See a bit more here:...

I'm not sure how others feel about this, but in my opinion using purge_dups depends on the overall assembly results. As @chhylp123 mentioned, the duplicated BUSCO genes could be real,...

> More to come on this. For now: `assignTaxonomy` with `minBoot=80` is recommended. Thanks, I'll give this a try > Furthermore, `assignTaxonomy` seems to work well for PacBio full-length 16S...

Hi @benjjneb I saw you had updated the SILVA138 with the long-read version of the `assignTaxonomy()` database (with species included). Thanks for adding that, we have a few data sets...

@EllaMae-O are these shotgun sequence data from the V1-V9 region, or the fragment ends alone (the regions next to, and possibly including, the primers)? The reason I ask, normally sequences...