GitHub topics: metabarcoding

Repositories

YSKoseki/gmmDenoise

A set of functions for effective ASV filtering in eDNA metabarcoding data on the basis of GMM

Language: R - Size: 1.13 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

pipecraft2/pipecraft

PipeCraft2 is a Graphical User Interface (GUI) for various metabarcoding pipelines

Language: JavaScript - Size: 179 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 1

nf-core/ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Language: Nextflow - Size: 16.6 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 197 - Forks: 132

ImagoXV/NanoASV

NanoASV official repo

Language: Shell - Size: 86.4 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 3

torognes/swarm

A robust and fast clustering method for amplicon-based studies

Language: C++ - Size: 5.1 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 134 - Forks: 23

torognes/vsearch

Versatile open-source tool for microbiome analysis

Language: C++ - Size: 8.4 MB - Last synced at: 11 days ago - Pushed at: 14 days ago - Stars: 695 - Forks: 127

icoia/microbiome_bioinformatics_analysis_2025

Metabarcoding and 16S rRNA Gene Sequencing (BIOF-Mic101)

Language: R - Size: 315 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0

pr2database/metapr2-shiny

Shiny application to access metaPR2 database

Language: R - Size: 400 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 3 - Forks: 1

vmikk/NextITS

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

Language: Nextflow - Size: 2.31 MB - Last synced at: 9 days ago - Pushed at: 15 days ago - Stars: 7 - Forks: 0

davidlougheed/snipe

A web tool for optimally choosing eDNA primer pairs to identify a set of taxa.

Language: TypeScript - Size: 916 KB - Last synced at: 4 days ago - Pushed at: 16 days ago - Stars: 3 - Forks: 0

benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

Language: R - Size: 468 MB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 489 - Forks: 146

pr2database/pr2database

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

Language: R - Size: 761 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 80 - Forks: 7

Next-ITS/next-its.github.io

NextITS pipeline documentation

Size: 7.62 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

adrientaudiere/MiscMetabar

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

Language: R - Size: 334 MB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 17 - Forks: 0

IrisRizos/Unassigned_Protists_SSN

Language: Python - Size: 440 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

quadram-institute-bioscience/dadaist2

Dadaist2 🟨 Highway to R

Language: HTML - Size: 40.6 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 5

quadram-institute-bioscience/dadaist1-docs

Legacy docs for Dadaist2 1.x

Size: 4.96 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

Newgenes1031/16S_PacBio_CCS_Metabarcoding_analysis_protocol

This is an easy guide of PacBio 16S metabarcoding analysis for amateur bioinformatician

Size: 0 Bytes - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

enormandeau/barque

eDNA metabarcoding pipeline

Language: Python - Size: 3.43 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 33 - Forks: 8

adriantich/MJOLNIR3

Metabarcoding Joining Obitools3 & Linkage Networks In R

Language: R - Size: 57.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

lexscience/Deep-oxygen-depleted-depressions-in-a-Red-Sea-coral-reef-sustain-resistant-ecosystems

Code and repository links for Klein & Frühe et al. 2024

Language: R - Size: 416 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

grunwaldlab/metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

Language: R - Size: 108 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 137 - Forks: 28

metabaRfactory/metabaR

metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.

Language: HTML - Size: 135 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 14 - Forks: 3

ManuelArcieri/Aqua-eDNA-metabarcoding-pipeline

A short pipeline for metabarcoding analyses and data visualisation

Language: Python - Size: 27.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

phylo42/PEWO

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

Language: Python - Size: 7.84 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 12 - Forks: 9

Mcouedel/mcouedel.github.io Fork of daattali/beautiful-jekyll

Dr Marion Couëdel's personal website

Language: HTML - Size: 15.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

erifa1/ranomaly

AmplicoN wOrkflow for Microbial community AnaLYsis

Language: HTML - Size: 39.8 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 0

sam-k/seq-quality-trimming

Trimming Sanger sequencing reads by quality

Language: Python - Size: 16.6 KB - Last synced at: 2 days ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 0

ClemSc/BLAST_2_LCA

Language: Python - Size: 95.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

nf-core/detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

Language: Nextflow - Size: 5.99 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 14 - Forks: 5

ANF-MetaBioDiv/course-material

Course material for the Action Nationale de Formation (ANF): Exploration de la diversité taxonomique des écosystèmes par metabarcoding

Language: HTML - Size: 104 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 4

AnneSoBen/obitools_workflow

A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.

Language: Python - Size: 64.5 KB - Last synced at: 8 days ago - Pushed at: 8 months ago - Stars: 4 - Forks: 2

VascoElbrecht/PrimerMiner

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Language: R - Size: 5.02 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 33 - Forks: 11

DominikBuchner/BOLDigger

A python package to query different databases of boldsystems.org

Language: Python - Size: 374 KB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 30 - Forks: 4

quadram-institute-bioscience/phylobarcode

<pilot> in-silico amplicons optimised for phylogenetic signal

Language: Python - Size: 563 KB - Last synced at: 5 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

nunofonseca/msi

Language: Shell - Size: 5.82 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 2

flefler/CyanoSeq

CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing

Size: 863 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 11 - Forks: 0

giorgiastaffoni/STREAM

Ballini & Staffoni et al. (submitted to Hydrobiologia) workflow

Language: Python - Size: 107 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

lougheedlab/eDNA_Manual

Language: Python - Size: 7.75 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

AmbrePetit/Metagenomics

The purpose of this repository is the metagenomic analysis of FastQ files

Language: Python - Size: 87.9 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

nwnoll/taxalogue

taxalogue - a toolkit to create comprehensive CO1 reference databases

Language: Ruby - Size: 882 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

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.

Language: Python - Size: 3.54 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 1

telatin/qax

Qiime2 Artifact eXtractor

Language: Nim - Size: 15.3 MB - Last synced at: about 2 months ago - Pushed at: 10 months ago - Stars: 5 - Forks: 1

JustJaxz/Region-Comparison-Pipeline

Scripts used to analyse metabarcoding data from two different gene regions to assess which provides a more complete picture of the eukaryotic marine microalgae community (EMC).

Language: R - Size: 1.34 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

marlaux/Metabarcoding-script-by-script

Former version of METAPIPE

Language: Shell - Size: 12.9 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

NRCan/Q2Pipe

Qiime2 based pipeline designed to facilitate and standardise ecological studies by metabarcoding using Illumina Miseq data

Language: Shell - Size: 4.05 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

robiwangriff/ENA-submission-in-R

R functions and workflow for submitting amplicon sequence data to the ENA.

Language: R - Size: 246 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

naturalis/barcode-constrained-phylogeny

Pipeline for building topologically-constrained phylogenies from DNA barcode data

Language: Python - Size: 3.32 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 3

AnneSoBen/MakeNGSfilter

Shiny app that creates files used by the OBITools to demultiplex metabarcoding sequences

Language: R - Size: 28.3 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ThibauldMichel/DADA2_Phyloseq

A DADA2 pipeline using rbcl markers libraries and a Phyloseq script to output graphical results.

Language: R - Size: 540 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

SushiLab/mTAGs

Language: Python - Size: 1.18 MB - Last synced at: 7 days ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 2

benjjneb/decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

Language: R - Size: 1.25 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 133 - Forks: 23

meghanmshea/intertidal-eDNA

Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)

Language: HTML - Size: 158 MB - Last synced at: 11 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

sbresnahan/metacleaner

Software for automated curation of barcode sequence databases for metabarcoding and metagenomics

Language: Python - Size: 87.9 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Public repository of data and analyses from Dirks and Jackson (2020), "Community structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy", Applied and Environmental Microbiology 86 (19)

Language: R - Size: 58.2 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

Hajibabaei-Lab/HajibabaeiEtAl2019

Datasets and code used to create figures in "Hajibabaei et al., 2019. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14(9): e0220953."

Language: R - Size: 2.65 MB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

DavideScarpetta/taxonomic_profiling

Metabarcoding analysis pipeline, using DADA2 and qiime2

Language: Shell - Size: 65.4 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Mycology-Microbiology-Center/Metabarcoding2022

Metabarcoding: from Lab to Bioinformatics (UT International Summer University, 2022)

Size: 421 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

phylo42/RAPPAS

Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences

Language: Java - Size: 47.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 3

eastmallingresearch/Metabarcoding_pipeline Fork of harrisonlab/Metabarcoding_projects

Metabarcoding pipeline

Language: R - Size: 768 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

gioche96/milk_microbiota

Repository for pipelines and scripts to analyse microbiota

Language: Shell - Size: 85.9 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

VascoElbrecht/JAMP

JAMP - Just Another Metabarcoding Pipeline

Language: R - Size: 6.71 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 31 - Forks: 6

CVUA-RRW/MetaSeqSim

Simulator of metabarcoding sequencing runs - Glorified ART wrapper

Language: Python - Size: 11.7 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

EcoBiomics-Zoobiome/SCVUC_COI_metabarcode_pipeline

Data flow to process COI metabarcodes

Language: Perl - Size: 41 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

lyy005/epps_nf

eDNA pipeline showcase

Language: Roff - Size: 18.2 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

GSMc-Fungi/GSMc-Fungi.github.io

The Global Soil Mycobiome consortium dataset

Size: 1.12 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

hjarnek/ReefPipe

Metabarcoding pipeline

Language: R - Size: 21.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Talitrus/bocas_eDNA

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Language: R - Size: 2.22 MB - Last synced at: 10 months ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 0

BenoitPAIX/Dactylospongia_metachromia_microbiome

A R script for the study of the prokaryotic community of the sponge Dactylospongia metachromia

Language: R - Size: 1.19 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

course-fish546-2023/Yerrace_metabarcoding

This is a repository for gut content DNA metabarcoding on invasive lionfish in the Caribbean. For the course FISH 546 Bioinformatics at SAFS

Language: HTML - Size: 48.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

HullUni-bioinformatics/Li_et_al_2019_eDNA_fish_monitoring

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

Language: R - Size: 3.51 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

terrimporter/CO1Classifier

This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

Size: 161 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 23 - Forks: 4

lucasmallet/cutting_ecm

Analysis of the effect of forestry cutting methods on ectomycorrhizal communities in boreal pine and spruce forest, using metabarcoding methods

Language: HTML - Size: 1.56 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

ifremer-bioinformatics/samba

Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

Language: Nextflow - Size: 109 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 5

jmpolinski/Moytirra-Hydrothermal-Vent-Plume

A primary goal of this research was to characterize vent plume biogeography across a spatial gradient. This study was done in collaboration with OceanX during the 2021 Young Explorers Program.

Language: R - Size: 54.8 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

CVUA-RRW/RRW-PrimerBLAST 📦

Retrieve sequences flanked by an arbitrary number of primers from a nucleotide collection.

Language: Python - Size: 25.4 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 2

molbiodiv/bcdatabaser

A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data

Language: Perl - Size: 1.32 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 3

EcoDynIZW/Axtner_2019_GigaScience Fork of alexcrampton-platt/screenforbio-mbc

"An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies"

Language: Shell - Size: 94.7 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

vaulot/R_tutorials

Tutorials for R

Language: HTML - Size: 31.4 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 5

gerverska/fun-gi

hamPCR + Douglas-fir + needle fungi

Language: HTML - Size: 96.3 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

CVUA-RRW/BAnalyzer 📦

Barcode Analyzer for metabarcoding experiments

Language: Python - Size: 34.2 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

metabarcoding 111 bioinformatics 26 edna 19 metagenomics 13 microbiome 11 pipeline 10 r 9 coi 9 co1 7 bioinformatics-pipeline 7 16s 7 workflow 7 amplicon-sequencing 7 fungi 7 taxonomy 7 amplicon 7 dna 6 ecology 6 nextflow 5 protists 5 database 5 taxonomic-classification 5 18s 5 edna-pipeline 5 environmental-dna 4 eukaryotes 4 dada2 4 taxonomy-assignment 4 r-package 4 pacbio 4 its 4 illumina 4 rrna 4 phyloseq 4 biodiversity 3 phylogenetic-placement 3 primer 3 18s-rrna 3 classification 3 mtdna 3 its1 3 clustering 3 freshwater 3 metabarcoding-pipeline 3 snakemake 3 taxonomic-profiling 3 qiime2 3 phylogenetics 3 fasta 2 vsearch 2 bacteria 2 archaea 2 asv 2 python 2 rdpclassifier 2 rdna 2 placement 2 nf-core 2 lakes 2 canopy 2 targeted-sequencing 2 phylo-kmers 2 docker 2 boldsystems 2 pcr 2 primers 2 microbiota 2 fastq 2 biochemistry 2 singularity 2 genomics 2 microbiome-analysis 2 blast 2 data-cleaning 2 oomycota 2 cercozoa 2 nanopore-analysis-pipeline 2 internal-transcribed-spacer 2 nanopore 2 metabarcoding-data 2 bioinformatics-analysis 2 sequencing 2 metatranscriptomics 1 hydrothermal-vent 1 deep-sea 1 primer-blast 1 idna 1 tutorials 1 compositional-data-analysis 1 endophyte 1 hampcr 1 high-throughput-sequencing 1 leaves 1 mycobiome 1 spatiotemporal 1 amf 1 arbuscular-mycorrhizal-fungi 1 mycology 1 cutadapt 1 genetic-markers 1