Here are
66 public repositories
matching this topic...
Versatile open-source tool for microbiome analysis
Accurate sample inference from amplicon data with single nucleotide resolution
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing 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 taxonomic identification
Updated
Apr 22, 2022
Python
A python package to query different databases of boldsystems.org
Updated
May 24, 2022
Python
🎨 dadaist2 - Highway to R
Updated
May 11, 2022
HTML
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Updated
Jun 2, 2022
Python
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
Updated
Apr 12, 2022
Java
Updated
Feb 15, 2021
HTML
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
Updated
Dec 8, 2021
Nextflow
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
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
Updated
Nov 10, 2021
Perl
metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
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
Analysis of 18S rRNA using the PR2 database
Qiime2 Artifact eXtractor
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
Nov 4, 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
Updated
Apr 23, 2020
Roff
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