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Here is a version of the pipeline "only_obitools" using snakemake workflow management system.

MOTU clustering and taxonomic assignation using SWARM method from eDNA NGS raw data

eDNA paired-end data analysis with assembly/demultiplexing tasks proceeded by VSEARCH/CUTADAPT and taxonomic assignation with ECOTAG

Here is a version of the pipeline "only_obitools" using nextflow, a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data.

Here, we reproduce the bioinformatics pipeline used by SPYGEN to generate species environmental presence from raw eDNA data.