metabarcoding
There are 107 repositories under metabarcoding topic.
torognes/vsearch
Versatile open-source tool for microbiome analysis
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
benjjneb/decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
grunwaldlab/metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
torognes/swarm
A robust and fast clustering method for amplicon-based studies
pr2database/pr2database
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
VascoElbrecht/JAMP
JAMP - Just Another Metabarcoding Pipeline
VascoElbrecht/PrimerMiner
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
terrimporter/CO1Classifier
This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
DominikBuchner/BOLDigger
A python package to query different databases of boldsystems.org
enormandeau/barque
Environmental DNA metabarcoding taxonomic identification
metabaRfactory/metabaR
metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
quadram-institute-bioscience/dadaist2
Dadaist2 🟨 Highway to R
adrientaudiere/MiscMetabar
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
phylo42/PEWO
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
bensutherland/eDNA_metabarcoding
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
flefler/CyanoSeq
CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
ifremer-bioinformatics/samba
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
nf-core/detaxizer
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.
phylo42/RAPPAS
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
CVUA-RRW/RRW-PrimerBLAST
Retrieve sequences flanked by an arbitrary number of primers from a nucleotide collection.
molbiodiv/bcdatabaser
A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
terrimporter/COI_NCBI_2018
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
vaulot/R_tutorials
Tutorials for R
pr2database/pr2-primers
Scripts for paper Vaulot et al. 2022
telatin/qax
Qiime2 Artifact eXtractor
vmikk/NextITS
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
RJauss/FromForestSoilToCanopy
Code and plots for the paper of Jauss & Walden et al., 2020, https://www.frontiersin.org/articles/10.3389/fmicb.2020.592189/
sam-k/seq-quality-trimming
Trimming Sanger sequencing reads by quality
AnneSoBen/obitools_workflow
A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.
CVUA-RRW/FooDMe
A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
Talitrus/bocas_eDNA
Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
terrimporter/18SClassifier
This repository contains 18S reference sets that can be used with the RDP Classifier to classify 18S rDNA metabarcode sequences.