Shareef Dabdoub

icon indicating a website link http://shareef.dabdoub.net icon indicating an email [email protected]

icon company University of Iowa icon location Iowa City, IA icon location Asst. Prof. University of Iowa. Division of Biostatistics and Computational Biology. Research focus on microbial ecology, multi-omics, data visualization

Results 24 comments of Shareef Dabdoub

It seems that unclassified reads are ignored

Hi Cedric, Since kraken-biom is written to collate reads assigned at various taxonomic levels, it does ignore reads that are marked as `Unclassified` in the kraken reports. Technically it shouldn't...

Bracken input error: "biom.exception.TableException: Cannot delimit self if I don't have data..."

Hi @trfeuerborn, I have not tried it yet with bracken files (although it has been on my list for a while). And you're the third person who's posted an issue...

Compatibility with krakenhll

Thanks for bringing KrakenHLL to my attention, I wasn't aware of it previously. The new format is the same with new columns inserted in the middle. Although your example appears...

Installation docs need to specify correct version of GTDB to download (max R214)

Manually updating the internal GTDB-tk conda environment to v2.4.0 does not appear to cause any issues.