Amplicon sequencing analysis workflow using DADA2 and QIIME2
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Updated
Oct 11, 2024 - Nextflow
Amplicon sequencing analysis workflow using DADA2 and QIIME2
desining block alignment geneotyper tags based on the whole genome alignment or gene alignment for phylogenomics
Ballini & Staffoni et al. (submitted to Hydrobiologia) workflow
Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies
A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.
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.
This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers
In this project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.
Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)
Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
Supporting codes for Manu et al., Ecological Indicators (2023). Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems
website of the otterconnect project
Primer scripts to produce meaningful visualisations from pre-processed metabarcoding data
Supplementary files for the paper "Environmental DNA metabarcoding of Danish soil samples reveals new insight into the hidden diversity of eutardigrades in Denmark"
This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
A set of functions for filtering erroneous sequences in eDNA metabarcoding data
"An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies"
TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data
metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
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