edna/snakemake_rapidrun_obitools

DNA Metabarcoding analyse on RAPIDRUN data with OBITOOLS encapsulated in SNAKEMAKE

Last synced at: 7 months ago - Stars: 0 - Forks: 2

edna/reference_database2

Last synced at: 7 months ago - Stars: 0 - Forks: 0

edna/snakemake_rapidrun_swarm

OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE

Last synced at: 7 months 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: 7 months ago - Stars: 0 - Forks: 0

edna/reference_database

Collection of scripts to build a reference database.

Last synced at: 7 months 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

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edna/GAPeDNA

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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.

Last synced at: 7 months 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: 7 months ago - Stars: 0 - Forks: 0

edna/query_metabarcoding_data

a shiny application to query information about our metabarcoding data

Last synced at: 7 months 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: 7 months 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: 7 months ago - Stars: 0 - Forks: 0

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

Last synced at: 7 months ago - Stars: 0 - Forks: 0