gitlab.mbb.cnrs.fr / edna 20 Dépôts
eDNA analysis scripts for the project MEGAFAUNA
edna/snakemake_rapidrun_obitools
DNA Metabarcoding analyse on RAPIDRUN data with OBITOOLS encapsulated in SNAKEMAKE
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edna/snakemake_rapidrun_swarm
OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
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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.
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edna/reference_database
Collection of scripts to build a reference database.
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edna/custom_reference_database
scripts to create our own reference database with our own sequences only and using the NCBI taxonomy
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edna/exploitation/primer_design
How to design a primer ?
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edna/snakemake_rapidrun_data_test
metabarcoding test data for snakemake rapidrun workflow
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edna/exploitation/primers_specificity_mismatchplot
Visualization of the specificity of designed primers with mismatch plot
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edna/exploitation/primer_specificity_ecopcr
This project permits to check the specificity of already designed primers.
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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.
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edna/query_metabarcoding_data
a shiny application to query information about our metabarcoding data
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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.
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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.
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edna/test_metabarcoding_data
data test to check metabarcoding workflow processing
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edna/exploitation/beginning_obitools
The first step to begin with obitools and Bash
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edna/tutorial_metabarcoding_data
Data for the tutorial on how to analyze DNA metabarcoding data produced on Illumina sequencers
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edna/metabarcoding_data_simulations
Simulations of metabarcoding data from fish 12S Teleo1
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edna/benchmark_pipelines
Comparison of multiple bioinformatic programs for each step of eDNA analysis
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