Oskar Hickl

Hi, would it have any unforseen consequences to remove https://github.com/tseemann/prokka/blob/c335b7a6539a960ff4d98af6d2c6eb9bc1b7ebde/bin/prokka#L690 ? It would be useful to get an output gff with all rows having uniform attribute fields starting with `ID`....

Trusted contigs with metaSPAdes

6

Hi, are there any plans to implement the use of trusted contigs with metaSPAdes? If not, why is it not possible? Cheers Oskar

Passing kwargs dict of dicts to modify catplot, manipulating stacked bar plot legend

2

Hi, first of all, thanks for making this, especially the recent addition of the stacked bar plots! Very nice documentation as well! One thing I am struggling with is the...

Assessing UMAP embedding quality and sweeping across n_neighbours parameter

3

Hi, I am very exicted to try to assess the quality of my embeddings using EMBEDR. I am unsure though how to set the `perplexity` value, while doing the `n_neighbours`...

UniProtTask:45 Unexpected error while requesting the service with query

4

Hi, I am trying out MPA portable with the example data to test if everything is working. It runs fine until the uniprot entries for the identified proteins are being...

Some errors I encountered

3

Hi Thilo, attached some errors I encountered while trying the two-step database search. Is there something I could improve with my setup or is it something with the MPA? Im...

Output only unmapped read of pair to --un-mates/conc, when only one maps

1

Hi I was wondering if it was possible to write only the unmapped read of a read pair to the unmapped output. It would be fine for me if the...

Guidance for working with large reference data sets

6

Hi, I am trying to build a database from RefSeq and GenBank genomes. The total size of the ~1.9 million compressed genomes is ~8.5T. Since the data set contains many...

GTDB 207 Kraken db vs maxikraken2_1903_140GB db classification rate

1

Hi, I have some trouble understanding the differences in classification rates between your GTDB 207 release Kraken database and the widely used maxikraken db from 2019, which is roughly half...

tRNAscan-SE slow with multiple threads

3

Hi, not sure where to go with this so I'll start here to ask if anyone experienced something similar since I use tRNAscan-SE with bakta. I noticed on tRNAscan-SE would...