The Wayback Machine - https://web.archive.org/web/20211011010208/https://github.com/topics/metabarcoding
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63 public repositories
matching this topic...
Versatile open-source tool for microbiome analysis
Accurate sample inference from amplicon data with single nucleotide resolution
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
A robust and fast clustering method for amplicon-based studies
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
JAMP - Just Another Metabarcoding Pipeline
This repository contains CO1 reference sets that can be used with the RDP Classifier to classify CO1 metabarcode sequences.
Environmental DNA metabarcoding analysis
Updated
Sep 23, 2021
Python
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Updated
Sep 9, 2021
Python
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
A python package to query different databases of boldsystems.org
Updated
Aug 17, 2021
Python
🎨 dadaist2 - Highway to R
Updated
Sep 22, 2021
HTML
Updated
Feb 15, 2021
HTML
This repository contains the scripts used to retrieve and analyze the data reported in Porter & Hajibabaei 2018 bioRxiv doi:
https://doi.org/10.1101/353904
A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
Updated
Aug 9, 2021
Nextflow
This repository contains 18S reference sets that can be used with the RDP Classifier to classify 18S rDNA metabarcode sequences.
Trimming Sanger sequencing reads by quality
Updated
Mar 7, 2019
Python
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
Data processing workflow and supplementary data for Li et al. 2019 - Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes
Updated
Apr 7, 2021
Shell
A python package to process UMI tagged mixed amplicon metabarcoding data.
Updated
Mar 20, 2021
Python
Supplementary files for Ribeiro et al. ISME 2018
Updated
Feb 26, 2020
Shell
Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
repository of data examples for the R package metabaR
Qiime2 Artifact eXtractor
Analysis of 18S rRNA using the PR2 database
Updated
Sep 13, 2021
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