Table 1 The contents of each reference database and instructions on how they were built
Database | Contents | Construction |
|---|---|---|
Hungate | Custom database containing 460 rumen microbial reference genomes from the Hungate collection (see Additional file 2: Table S3) | For file in /hungate_genomes/*.fasta do kraken2-build --add-to-library $file --db hungate_only_db_k2 done kraken2-build --build --threads 16 --db hungate_only_db_k2 |
Mini | The complete collection of genomes in RefSeq for bacterial, viral and archaeal domains, the human genome and UniVec_Core vectors. The database was built to 8 GB in size to replicate the “MiniKraken” functionality of Kraken1 | kraken2-build --download-library bacteria --db mini_standard_db_k2 --use-ftp kraken2-build --download-library archaea --db mini_standard_db_k2 --use-ftp kraken2-build --download-library viral --db mini_standard_db_k2 --use-ftp kraken2-build --download-library human --db mini_standard_db_k2 --use-ftp kraken2-build --download-library UniVec_Core --db mini_standard_db_k2 --use-ftp kraken2-build --db mini_standard_db_k2 --build --max-db-size 8,000,000,000 --threads 4 |
RefSeq | The complete collection of genomes in RefSeq for bacterial, viral and archaeal domains, the human genome and UniVec_Core vectors | kraken2-build --download-library bacteria --db standard_db_k2 --use-ftp kraken2-build --download-library archaea --db standard_db_k2 --use-ftp kraken2-build --download-library viral --db standard_db_k2 --use-ftp kraken2-build --download-library human --db standard_db_k2 --use-ftp kraken2-build --download-library UniVec_Core --db standard_db_k2 --use-ftp kraken2-build --build --threads 16 --db standard_db_k2 |
RUG | Custom database containing 4,941 rumen metagenome-assembled genomes (named “RUGs” - see Stewart et al. [17]) | For file in /rug_drafts/*.fna do kraken2-build --add-to-library $file --db rug2_only_db_k2 done kraken2-build --build --threads 8 --db rug2_only_db_k2 |
RefRUG | The complete collection of genomes in RefSeq for bacterial, viral and archaeal domains, the human genome and UniVec_Core vectors with the addition of 4,941 rumen metagenome-assembled genomes (named “RUGs” - see Stewart et al. [17] and the RUG database) | kraken2-build --download-library bacteria --db standard_rug2_db_k2 --use-ftp kraken2-build --download-library archaea --db standard_rug2_db_k2 --use-ftp kraken2-build --download-library viral --db standard_rug2_db_k2 --use-ftp kraken2-build --download-library human --db standard_rug2_db_k2 --use-ftp kraken2-build --download-library UniVec_Core --db standard_rug2_db_k2 --use-ftp for file in /rug_drafts/*.fna do kraken2-build --add-to-library $file --db standard_rug2_db_k2 done kraken2-build --build --threads 16 --db standard_rug2_db_k2 |
RefHun | The complete collection of genomes in RefSeq for bacterial, viral and archaeal domains, the human genome and UniVec_Core vectors with the addition of 460 reference genomes from the Hungate collection (see Hungate database section of this table and Additional file 2: Table S3) | kraken2-build --download-library bacteria --db standard_hungate_db_k2 --use-ftp kraken2-build --download-library archaea --db standard_hungate_db_k2 --use-ftp kraken2-build --download-library viral --db standard_hungate_db_k2 --use-ftp kraken2-build --download-library human --db standard_hungate_db_k2 --use-ftp kraken2-build --download-library UniVec_Core --db standard_hungate_db_k2 --use-ftp for file in /hungate_genomes/*.fasta do kraken2-build --add-to-library $file --db standard_hungate_db_k2 done kraken2-build --build --threads 16 --db standard_hungate_db_k2 |
HunRUG | The 460 reference genomes from the Hungate collection (see Hungate database section of this table and Additional file 2: Table S3), and 4,941 rumen metagenome-assembled genomes (named “RUGs” - see Stewart et al. [17] and the RUG and RefRUG databases). | For file in /hungate_genomes/*.fasta do kraken2-build --add-to-library $file --db hungate_rug2_db_k2 done For file in /rug_drafts/*.fna do kraken2-build --add-to-library $file --db hungate_rug2_db_k2 done kraken2-build --build --threads 16 –db hungate_rug2_db_k2 |
RefHunRUG | The complete collection of genomes in RefSeq for bacterial, viral and archaeal domains, the human genome and UniVec_Core vectors with the addition of 460 reference genomes from the Hungate collection (see Hungate database section of this table and Additional file 2: Table S3), and 4,941 rumen metagenome-assembled genomes (named “RUGs” - see Stewart et al. [17] and the RUG and RefRUG databases). | kraken2-build --download-library bacteria --db standard_hungate_rug2_db_k2 --use-ftp kraken2-build --download-library archaea --db standard_hungate_rug2_db_k2 --use-ftp kraken2-build --download-library viral --db standard_hungate_rug2_db_k2 --use-ftp kraken2-build --download-library human --db standard_hungate_rug2_db_k2 --use-ftp kraken2-build --download-library UniVec_Core --db standard_hungate_rug2_db_k2 --use-ftp For file in /hungate_genomes/*.fasta do kraken2-build --add-to-library $file --db standard_hungate_rug2_db_k2 done For file in /rug_drafts/*.fna do kraken2-build --add-to-library $file --db standard_hungate_rug2_db_k2 done kraken2-build --build --threads 16 --db standard_hungate_rug2_db_k2 |