OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
Here is a version of the pipeline "only_obitools" using snakemake workflow management system.
DNA Metabarcoding analyse on RAPIDRUN data with OBITOOLS encapsulated in SNAKEMAKE
eDNA paired-end data analysis with assembly/demultiplexing tasks proceeded by VSEARCH/CUTADAPT and taxonomic assignation with ECOTAG
MOTU clustering and taxonomic assignation using SWARM method from eDNA NGS raw data
Collection of scripts to build a reference database.
scripts to create our own reference database with our own sequences only and using the NCBI taxonomy
Workflow Application Wrapper
Shiny App Generator
Code used by https://mbb.univ-montp2.fr/MBB/dnabushmeat
data test to check metabarcoding workflow processing