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

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

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.

Simulator of metabarcoding sequencing runs - Glorified ART wrapper

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).

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

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

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

This workflow performs a metabarcoding analysis from the reads sequencing to the production of a report presenting the graphical results.