Dataset from Zenodo · Hall, Michael B.
Mycobacterium representative kraken2 database
- License
- CC0 1.0commercial use allowedLicense text
- This license allows commercial use. Usually you must credit the author; read the license for the exact terms.
- Formats
- GZ, TXT, PY
- Size
- 6.2 GB
- Updated
- Feb 15, 2024
Description
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…
Description from Zenodo, shortened.
Files (3)
- GZk2_Mycobacterium_20230817.tar.gz6.2 GB
- TXTassembly_summary.txt707 kB
- PYprepare_kraken_fasta.py2.8 kB
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