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.
MOTU clustering and taxonomic assignation using SWARM method from eDNA NGS raw data
Here, we reproduce the bioinformatics pipeline used by SPYGEN to generate species environmental presence from raw eDNA 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 snakemake workflow management system.