Christopher Gulvik

This is a bit hackish but works without modifying the `ngd` package. If you invoke the `--human-readable` option, you'll get `./human_readable/{genbank,refseq}/////.gbff.gz` so you can make symlinks off of those path...

@sfchen Any thoughts on this reporting? I just ran into another case where this would be valuable (wrongly entered indices). A non-default if you're after speed for routine would be...

> Ultimately it should not matter what reference you use, because the SNPs it generates are "core" only. One reason I'd like to specify a ref is faster processing of...

You likely lack some of the scripts that are from CG-pipeline though. I don't think there's a test for all binary and script availability ran at the end (executing `launch_set.pl...

Agreed MSA isn't an obvious outdir. Maybe a _summary_stats_ file to indicate _%reads mapped_ for each sample (example script attached that I use for lyve-SET), _% ref genome length_ (how...

@lawremi This could be useful to overlay coverage of long and short reads from the same gDNA sample. Coverage is likely to be quite different (Y-axis), so I think you'd...

@Midnighter Any progress on this? I'm also interested in having it for evaluation. According to the docs `sourmash tax` is the recommended approach (not `sourmash lca` anymore) [link](https://sourmash.readthedocs.io/en/latest/classifying-signatures.html#sourmash-tax-vs-sourmash-lca). I don't...

This is a hackish workaround to accomplish it for type strains for the time being. ``` git clone [email protected]:lmc297/BTyper3.git mkdir -p Btyper3/seq_ani_db/typestrains awk '{print $1 "\t" $3}' \ Btyper3/seq_ani_db/typestrains/typestrains.tsv \...

FYI this is a super fast and useful Genus-level 16S rRNA gene classifier tool. Part of the reason the container is bigger than most is it includes the database file...

> I'm trying to provide some guidance on a CMD layer. This would be the default command that runs when given no arguments (i.e. docker run staphb/rdp:latest). Generally we use...