Supporting digital resources and scripts for the Porter et al., 2024 publication.

Scripts and files to support the pseudogene manuscript.

Miscellaneous colleciton of Perl, Python, Shell, and R scripts

Supporting digital resources and scripts for the Porter et al., 2023 Sci Rep 13:7978 publication.

MetaWorks is a flexible multi-marker metabarcode pipeline for processing paired-end Illumina reads from raw fastq.gz files to taxonomic assignments.

International eDNA Standardization Task Force

This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

This repository contains 12S mitochondrial gene reference sets that can be used with the RDP Classifier to classify 12S metabarcode sequences from fish.

The plant PLANiTS ITS reference set formatted for the Ribosomal Database Project (RDP) classifier.

Fungal UNITE ITS reference set formatted for the Ribosomal Database Project (RDP) classifier.

Infiles and scripts written by Chloe Robinson and Terri Porter to reproduce figures in the Robinson et al., 2020 paper.

This repository contains rbcL reference sets that can be used with the RDP Classifier to classify rbcL metabarcode sequences.

This repository contains 18S reference sets that can be used with the RDP Classifier to classify 18S rDNA metabarcode sequences.

This repository contains SSU rDNA reference sets that can be used with the RDP Classifier to classify SSU rDNA metabarcode sequences from diatoms.

This repository contains rbcL cpDNA reference sets that can be used with the RDP Classifier to classify rbcL cpDNA metabarcode sequences from diatoms.

Data flow to process 18S rDNA metabarcodes

Data flow to process 16S metabarcodes.

Snakemake bioinformatic pipeline to process rbcL cp DNA metabarcodes

Data flow to process ITS metabarcodes

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

Porter et al., 2019 Scientific Reports, 9: 18218 data files and scripts

Data flow and scripts used to process COI metabarcodes. Reads are paired, primers are trimmed, reads are denoised in a global analysis, then they are taxonomically assigned.