Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
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Updated
May 15, 2024 - Python
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Environmental DNA metabarcoding taxonomic identification
A python package to query different databases of boldsystems.org
Pipeline for building topologically-constrained phylogenies from DNA barcode data
Retrieve sequences flanked by an arbitrary number of primers from a nucleotide collection.
A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.
A python package to process UMI tagged mixed amplicon metabarcoding data.
A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
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).
This workflow performs a metabarcoding analysis from the reads sequencing to the production of a report presenting the graphical results.
Ballini & Staffoni et al. (submitted to Hydrobiologia) workflow
Trimming Sanger sequencing reads by quality
The purpose of this repository is the metagenomic analysis of FastQ files
A tool to select the best primers to perform quantitative metabarcoding studies.
Simulator of metabarcoding sequencing runs - Glorified ART wrapper
Barcode Analyzer for metabarcoding experiments
Software for automated curation of barcode sequence databases for metabarcoding and metagenomics
<pilot> in-silico amplicons optimised for phylogenetic signal
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