Eco-Flow/nanoporemetabarcoding is a Nextflow pipeline -written using the nf-core standards- for processing -quality control, demultiplexing, and clustering- and annotate nanopore metabarcoding data. Annotation is performed at different taxonomic levels on the consensus sequences, using the BLASTnt database and taxonomizr.
Overview
Overall, the pipeline performs the following steps:
- Performs read filtering, trimming, and quality control on both raw and processed sequencing reads.
- Demultiplexes reads based on tag–primer combinations
- Groups amplicon reads into ‘species’ consensus sequences
- Annotates consensus sequences based on the best matching reference hit against BLAST database
- Assigns taxonomy to annotated sequences using NCBI taxonomy identifiers
For additional details, usage instructions, and examples, please refer to the Eco-Flow/nanoporemetabarcding GitHub repository.