This page serves as a hub that makes it easy to find the most widely used code and public data from the Kartzinel Lab.
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Hot off the press!
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Code to quantify and characterize the number of unique 'diet types' that exist within a population or community. The strategy is based on a simple machine-learning algorithm and described in the Hoff et al. 2025 PNAS paper.
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Evaluate how different 'diet types' contribute to variation in the foraging of wildlife populations using the method of Hoff et al. 2025.
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Featured Software
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Quantify the availability of plant DNA barcodes to support basic and policy-relevant biodiversity research. We provide a customizable Code Book, as described in our 2025 Molecular Ecology review.
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The contribution of our Yellowstone Plant DNA Barcode Library to global plant DNA barcode availability (Kartzinel et al. 2025). |
Access Our Open-Source Code Repositories
*New* October 2025
New code to help generate standardized sets of data summaries and tables for your manuscripts and data archives.
Learn more: "Step 5" of our Dietary DNA Metabarcoding Pipeline
New code to help generate standardized sets of data summaries and tables for your manuscripts and data archives.
Learn more: "Step 5" of our Dietary DNA Metabarcoding Pipeline
Dietary DNA Metabarcoding Pipeline
Our open-source, flexible pipeline for dietary DNA metabarcoding based on Illumina data. For an overview of this five-part pipeline, please check out this complete roadmap of how these parts fit together.
Pre-processing Steps for Raw Sequence Data
Download the code that we use to run our standard quality checks and reporting pipeline from this GitHub repository. This repository helps organize raw sequence data for efficient analysis, generate summary statistics to report in publications, and prepare data for permanent archiving (e.g., with NCBI). We refer to this part of the pipeline as "Step 1a-c."
Formatting a 'Global' DNA Barcode Library for Obitools
Download the code that we use to prepare a global DNA barcode reference library from this Github repository. This repository uses data from the European Nucleotide Archive (ENA) for a given group of taxa and formats the reference set for use in Obitools2. This code works flexibly so you can build custom libraries for any biological grouping. Below, we provide links to several popular and pre-made libraries for plants and animals that we use frequently in the lab. We refer to this part of the pipeline as "Step 2a."
Building a 'Local' DNA Barcode Library using BOLD
Download the code that we use to prepare a local DNA barcode reference library from this Github repository. The code will help you prepare a local DNA barcode reference library based on any project you build using the Barcode of Life Data Systems platform (BOLDsystems.org). This reference set can be formatted for use in Obitools2 and we find it very helpful for corroborating and/or refining gross taxonomic inferences obtained based on globally available data. The sequences included do not have to be generated 'locally' but should be curated to ensure project relevance. We refer to this optional part of the pipeline as "Step 2b."
Inferring Taxonomy Based on DNA Metabarcode Data
We provide a suite of steps to annotate DNA metabarcoding data, screen them for potential errors, and infer the taxonomy of all sequence reads that are obtained in this GitHub repository. We refer to this part of the pipeline as "Step 3." After cleaning the dataset, we format results for downstream analyses in the R package 'phyloseq.' There are options in "Step 4" of the pipeline depending on whether one or more reference libraries were used in the analysis.
Preparing Data Tables for Analyses & Publication
The newest module of utilities we provide at this GitHub repository is useful to perform additional quality checks using the R package 'phyloseq' as you prepare for analyses. Our workflow includes parsing samples, rarefying to equal sequencing depth, and merging data with additional taxonomic or ecological metadata. What makes this code most helpful is that it provides comprehensive data summaries and exports both formatted tables you can use for manuscript submission. We call this "Step 5" as our workflow transitions from data-processing toward analysis of the resulting dataset.
Access Our Ready-to-Use DNA Barcode Libraries
Global Plant trnL-P6 g/h Database
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Yellowstone Plant DNA Barcode Library
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Fray Jorge Plant DNA Barcode Library
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