This repository contains all project files, including scripts, results, and articles. It was developed for the UC project included in the bioinformatics master's program for 2023-2024.
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Updated
May 23, 2024 - R
This repository contains all project files, including scripts, results, and articles. It was developed for the UC project included in the bioinformatics master's program for 2023-2024.
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
The purpose of this repository is the metagenomic analysis of FastQ files
Versatile open-source tool for microbiome analysis
Former version of METAPIPE
Environmental DNA metabarcoding taxonomic identification
Pipeline for building topologically-constrained phylogenies from DNA barcode data
PipeCraft2 is a Graphical User Interface (GUI) for various metabarcoding pipelines
Qiime2 based pipeline designed to facilitate and standardise ecological studies by metabarcoding using Illumina Miseq data
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
R functions and workflow for submitting amplicon sequence data to the ENA.
Shiny app that creates files used by the OBITools to demultiplex metabarcoding sequences
A DADA2 pipeline using rbcl markers libraries and a Phyloseq script to output graphical results.
Metabarcoding Joining Obitools3 & Linkage Networks In R
A robust and fast clustering method for amplicon-based studies
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.
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)
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