Amplicon sequencing analysis workflow using DADA2 and QIIME2
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Updated
May 9, 2024 - Nextflow
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies
This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.
metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.
Data processing workflow and supplementary data for Li et al. 2018 - The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding
TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data
repository of data examples for the R package metabaR
Primer scripts to produce meaningful visualisations from pre-processed metabarcoding data
This is a Jupyter Notebook to make phylogenetic trees with the Open Tree of Life from a list of taxa such as those from Anacapa output (CALeDNA format)
Data & Code Supplement for "Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems"
Supplementary files for the paper "Environmental DNA metabarcoding of Danish soil samples reveals new insight into the hidden diversity of eutardigrades in Denmark"
Official GitHub repository for the R package "Species Identity and Evolution in R" (spider)
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