Sofia Stamouli
Sofia Stamouli
`Pychopper` is for cDNA reads so not useful for us. I will have to test first but to my understanding, we can use `porechop_abi `as optional step for adapter trimming...
I approve, shall but shall we merge the template first?
@pirovc Thanks for letting us know!
From slack: https://github.com/PacificBiosciences/pb-metagenomics-tools/blob/master/docs/Tutorial-Taxonomic-Profiling-Diamond-Megan.md Similar to kraken2 and bracken structure?
Thanks for the quick review.
Tests are not passing for taxpasta, the output formats are the same in the newest version so it should not have been an issue, looking closer into this. ![Screenshot 2024-02-08...
I tested locally with the minimal data and no issue with taxpasta `nextflow run main.nf -profile test,docker --run_ganon --outdir test_ganon_output -resume` The ganon files look ok. I will run the...
I do not have experience with KrakenUniq but I came across this discussion in their github repo https://github.com/fbreitwieser/krakenuniq/issues/112
Regarding `kaiju`: https://github.com/bioinformatics-centre/kaiju/issues/209#issuecomment-1020019707
I was thinking of playing around first and if we should consider a default parameter for kaiju.