DRGM: Kraken2 databases

This record contains two custom databases compatible with Kraken2 and Bracken, built from the DRGM species with k = 35. The metadata tables, genome sequences, protein catalogs, antibiotic resistance gene predictions, and species pangenomes of this catalog are deposited as separate records. Kraken2 database File list DRGM_kraken2_concat.tar.gz : built from all genomes of each species, concatenated per species DRGM_kraken2_representative.tar.gz : built from the representative genome of each species Each archive contains a complete database directory: DRGM_kraken2_concat/ hash.k2d opts.k2d taxo.k2d seqid2taxid.map taxonomy/ names.dmp nodes.dmp library/ library.fna database64mers.kmer_distrib database70mers.kmer_distrib database77mers.kmer_distrib database90mers.kmer_distrib database100mers.kmer_distrib database125mers.kmer_distrib database136mers.kmer_distrib database150mers.kmer_distrib database250mers.kmer_distrib Bracken distributions are provided for nine read lengths: 64, 70, 77, 90, 100, 125, 136, 150 and 250 bp. library/library.fna holds the sequences the database was built from, wrapped at 60 characters per line. Usage - pass the extracted directory as the database: tar -xzf DRGM_kraken2_concat.tar.gz kraken2 --db DRGM_kraken2_concat --paired sample_1.fq.gz sample_2.fq.gz --report sample.kreport --output sample.kraken bracken -d DRGM_kraken2_concat -i sample.kreport -o sample.bracken -r 150 -l S