Map metagenomic reads to operational taxonomic units (OTUs) using kraken2 and estimate bacterial abundances with bracken.
- Set up nextflow as described here.
- If you didn't run this pipeline in a while, possibly update nextflow itself.
./nextflow self-update - Then run the pipeline.
./nextflow run https://github.com/UnseenBio/bracken-nf
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- Free software distributed under the GNU Affero General Public License version 3.