Here, we reproduce the bioinformatics pipeline used by SPYGEN to generate species environmental presence from raw eDNA data.
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
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.
eDNA paired-end data analysis with assembly/demultiplexing tasks proceeded by VSEARCH/CUTADAPT and taxonomic assignation with ECOTAG