Lars Snipen

Large number of genomes

3

First, a suggestion: It would be very helpful to be able to turn off the screen output. We use fastANI with a single query genome against a long list (thousands)...

I have used mash dist a lot, with good results. Now I want to use mash screen, and find that here I sketch the genomes, but not the metagenome? It...

suboptimal alignment when matching the end of the reference (in blast output)

18

It looks to me that SortMeRNA consistently output wrong coordinates in the blast format when the alignment runs across the end of the subject sequence (rRNA). Assume we have a...

Segmentation fault in step 1 (seqid2taxid parsing)

2

I have made a kraken2 database, and it works fine. However, when trying to build a bracken database from this I get a segmentation fault, and I believe it occurs...

Slow building of GTDB database

8

Hi, Thanks for this tool, this is something I have looked forward to. But, I have some questions. I have downloaded the pre-built GTDB database, and it works fine. However,...

tax_id's overlapping with NCBI

5

Hi, I need to combine the GTDB taxonomy under domains Archaea and Bacteria with the NCBI taxonomy of everything else (eukaryote, virus). However, with the GTDB R226 taxdump files I...