eDNA metabarcoding pipeline

A python package to query different databases of boldsystems.org

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

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

Trimming Sanger sequencing reads by quality

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

A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.

Pipeline for building topologically-constrained phylogenies from DNA barcode data

A python package to process UMI tagged mixed amplicon metabarcoding data.

A tool to select the best primers to perform quantitative metabarcoding studies.

Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).

Simulator of metabarcoding sequencing runs - Glorified ART wrapper

A short pipeline for metabarcoding analyses and data visualisation

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

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

Barcode Analyzer for metabarcoding experiments