inspect‐kraken2‐db

This method generates a report of identical format to those generated by classify_kraken2, with the interpretation being instead of reporting the number of inputs classified to a taxon/clade, the number of minimizers mapped to a taxon/clade are reported.

For the full description of the action's inputs, outputs, and parameters run qiime moshpit inspect‐kraken2‐db --help in the terminal.

Inputs

• db (Kraken2DB): The Kraken 2 database for which to generate the report.

Outputs

• report (Kraken2DBReport): The report of the supplied database.

Example Use

qiime moshpit inspect-kraken2-db \
   --i-db db.qza \
   --o-report report.qza \
   --verbose

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}
}