Lee Katz

Have an option to write to a file or files what fasten_trim removes. Maybe an output directory since it will be undoubtedly just be intermediate files.

numcpus does not work

10

Need to add functionality for numcpus

`Salmonella enterica IIIa UGXG01000002` seems to have a lot of premature stops. Might want to switch it out.

Seems to be an important gut bacterium txid1678[Organism] AND (latest[filter] AND "chromosome level"[filter] AND all[filter] NOT anomalous[filter] AND "genbank has annotation"[Properties]) This paper lists a few species that might be...

Need to add C. hastiforme

1

Is closely related to C. bot and C. sporogenes but is its own species

It was a recent contaminant or mix up in one sample

Hops shares the same family as cannabis too Here is a probably good mitochondrial genome to add https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_963169125.1/

It might be worth mentioning that the kraken-build creates the .k2d files and seqid2map files for a valid database. It doesn’t require anything else.

Chromosome of subspecies IV

5

Salmonella enterica CP053576 might be the incorrect entry and I'll need to double check that. It might be the plasmid of subspecies IV and not the chromosome.

Need to change Escherichia hermannii to the new genus name Atlantibacter. Already done in `development.tsv`. Need to do it in the taxonomy files too.