estimate‐bracken - bokulich-lab/q2-annotate GitHub Wiki

Perform read abundance re-estimation using Bracken.

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

Inputs

• kraken_reports (SampleData[Kraken2Reports % Properties('reads')]): Reports produced by Kraken2.
• bracken_db (BrackenDB): Bracken database.

Outputs

• reports (SampleData[Kraken2Reports % Properties('bracken')]): Reports modified by Bracken.'
• taxonomy (FeatureData[Taxonomy])): TODO
• table (FeatureTable[Frequency]): TODO

Example Use

qiime moshpit estimate-bracken \
--i-bracken-db bracken_db.qza \
--i-kraken-reports reports \ # folder with SampleData[Kraken2Reports % Properties('reads')] artifacts
--o-reports reports_bracken \ # output folder
--o-table table.qza \
--o-taxonomy taxonomy.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}
}