build‐kraken‐db

This method builds a Kraken-2/Bracken database from provided DNA sequences or simply fetches pre-built versions from an online resource.

• For the full description of the action's inputs, outputs and parameters run qiime moshpit build‐kraken‐db --help in the terminal.

Inputs

• seqs (List[FeatureData[Sequence]]): This input is optional. Sequences to be added to the Kraken 2 database.

Outputs

• kraken2_database (Kraken2DB): Kraken2 database.
• bracken_database (BrackenDB): Bracken database.

Citation

@article{key0,
 author = {Wood, Derrick E. and Lu, Jennifer and Langmead, Ben},
 doi = {10.1186/s13059-019-1891-0},
 issn = {1474-760X},
 journal = {Genome Biology},
 keywords = {Alignment-free methods, Metagenomics, Metagenomics classification, Microbiome, Minimizers, Probabilistic data structures},
 month = {nov},
 number = {1},
 pages = {257},
 title = {Improved metagenomic analysis with Kraken 2},
 url = {https://doi.org/10.1186/s13059-019-1891-0},
 urldate = {2023-01-17},
 volume = {20},
 year = {2019}
}

@article{key1,
 author = {Lu, Jennifer and Breitwieser, Florian P. and Thielen, Peter and Salzberg, Steven L.},
 doi = {10.7717/peerj-cs.104},
 issn = {2376-5992},
 journal = {PeerJ Computer Science},
 month = {January},
 pages = {e104},
 publisher = {PeerJ Inc.},
 shorttitle = {Bracken},
 title = {Bracken: Estimating Species Abundance in Metagenomics Data},
 volume = {3},
 year = {2017}
}