classify‐kaiju

Classify reads using Kaiju.

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

Inputs

• seqs (SampleData[SequencesWithQuality] | SampleData[PairedEndSequencesWithQuality]): Sequences to be classified.
• db (KaijuDB): Kaiju database.

Outputs

• abundances (FeatureTable[Frequency]): Read abundances.
• taxonomy (FeatureData[Taxonomy]): Linked taxonomy.

Example Use

qiime moshpit classify-kaiju \
   --i-db kaiju_db.qza \
   --i-seqs seqs.qza \
   --o-abundances abundancs.qza \
   --o-taxonomy taxnomy.qza \
   --verbose 

Citation

@article{key0,
 author = {Menzel, Peter and Ng, Kim Lee and Krogh, Anders},
 doi = {10.1038/ncomms11257},
 issn = {2041-1723},
 journal = {Nature Communications},
 keywords = {Classification and taxonomy,Metagenomics},
 month = {April},
 number = {1},
 pages = {11257},
 publisher = {Nature Publishing Group},
 title = {Fast and Sensitive Taxonomic Classification for Metagenomics with Kaiju},
 volume = {7},
 year = {2016}
}