Mycobacterium representative kraken2 database

A kraken2 database built from the a representative Mycobacterium set of genomes. This archive contains the three files required by kraken2, hash.k2d, opts.k2d, and taxo.k2d, along with inspect.txt, which is obtained by running kraken2-inspect on the database.

The genomes for this database were downloaded wiuth genome_updater.sh (v0.6.3; https://github.com/pirovc/genome_updater) with one RefSeq genome from each species in the Mycobacteriaceae family, plus one RefSeq genome from each species in the following genera: Klebsiella, Escherichia, Salmonella, Enterobacter, Streptococcus, Staphylococcus, Pseudomonas, Xanthomonas, and Bifidobacterium.

genome_updater.sh -A "species:1" -m -a -M "gtdb" -f "genomic.fna.gz" -g "bacteria" -d "refseq" -T "f__Mycobacteriaceae,g__Klebsiella,g__Escherichia,g__Enterobacter,g__Salmonella,g__Streptococcus,g__Staphylococcus,g__Pseudomonas,g__Xanthomonas,g__Bifidobacterium" -o GTDB_Mycobacterium/

The python script prepare_kraken_fasta.py was then used to prepare the assemblies for use in kraken with the following command

python prepare_kraken_fasta.py -r -x GCF_932530395.1,GCF_017190695.1,GCF_020735285.1,GCA_014701265.1,GCF_000013925.1,GCF_016756075.1,GCF_010727125.1,GCF_001307545.1 -o Mycobacterium.fna -s assembly_summary.txt GTDB_Mycobacterium/

The database was then built with kraken2 using the following commands

kraken2-build --download-taxonomy --db db/
kraken2-build --add-to-library Mycobacterium.fna --db db/
kraken2-build --build --db db/ --threads 16