gitlab.mbb.cnrs.fr / edna 20 Repositories
eDNA analysis scripts for the project MEGAFAUNA
edna/snakemake_rapidrun_obitools
DNA Metabarcoding analyse on RAPIDRUN data with OBITOOLS encapsulated in SNAKEMAKE
Last synced at: about 1 year ago - Stars: 0 - Forks: 2
edna/snakemake_rapidrun_swarm
OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/edna_intra_pipeline_comparison
This project aims to compare twelve bioinformatics pipelines based on five existing metabarcoding programs to make recommendations for data management in intraspecific variability studies using environmental DNA.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/reference_database
Collection of scripts to build a reference database.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/custom_reference_database
scripts to create our own reference database with our own sequences only and using the NCBI taxonomy
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/primer_design
How to design a primer ?
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/snakemake_rapidrun_data_test
metabarcoding test data for snakemake rapidrun workflow
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/primers_specificity_mismatchplot
Visualization of the specificity of designed primers with mismatch plot
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/primer_specificity_ecopcr
This project permits to check the specificity of already designed primers.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/dada2_and_obitools
This project has for goal to filtrate efficiently eDNA sequences after PCR amplification and NGS, in order to eliminate the false sequences generated by these technologies.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/query_metabarcoding_data
a shiny application to query information about our metabarcoding data
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/swarm_and_obitools
This project is based on the idea that gathering similar sequences allows to faithfully study them by eliminating sequences generated from PCR or NGS errors.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/only_obitools
This project presents a pipeline based on OBITools commands in order to eliminate sequences interpreted as coming from PCR errors and to assign each remaining sequence to a taxon thanks to a reference database.
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/test_metabarcoding_data
data test to check metabarcoding workflow processing
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/exploitation/beginning_obitools
The first step to begin with obitools and Bash
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/tutorial_metabarcoding_data
Data for the tutorial on how to analyze DNA metabarcoding data produced on Illumina sequencers
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/metabarcoding_data_simulations
Simulations of metabarcoding data from fish 12S Teleo1
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
edna/benchmark_pipelines
Comparison of multiple bioinformatic programs for each step of eDNA analysis
Last synced at: about 1 year ago - Stars: 0 - Forks: 0
