classify‐kraken2

This method uses Kraken 2 to classify provided NGS reads or MAGs into taxonomic groups.

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

Inputs

• seqs (SampleData[SequencesWithQuality] | SampleData[PairedEndSequencesWithQuality] | SampleData[Contigs]|FeatureData[MAG]): Sequences to be classified. Both, single-/paired-end reads and assembled MAGs, can be provided.
• kraken2_db (Kraken2DB): Kraken 2 database.

Outputs

• reports (SampleData[Kraken2Reports] | FeatureData[Kraken2Reports]): Reports produced by Kraken2.
• hits (SampleData[Kraken2Outputs] | FeatureData[Kraken2Outputs]): Output files produced by Kraken2.

Example Use

qiime moshpit classify-kraken2 \
   --i-seqs seqs.qza \
   --i-kraken2-db kraken_db.qza \
   --o-hits hits \ # output folder
   --o-reports reports \ # output folder
   --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}
}