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12sfishclassifier

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

12svertebrateclassifier

16svertebrateclassifier

18sclassifier

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

chronosequence

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

co1classifier

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

coi_ncbi_2018

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

erdozainetal2018

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.

helperscripts_2023-12-28

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

iestf

International eDNA Standardization Task Force

introbiodiversityanalysis2022

jessehoage2018

This repository contains the scripts used to process Illumina MiSeq 18S, ITS2, and CO1 metabarcodes for Jesse Hoage's Master's thesis (2018). The ammended CO1 reference set is also included here (CO1 Classifier v2.1).

johnsonetal2020

mahmoudietal2013

Code that was used to generate figures for the Mahmoudi et al., 2013 publication

metaworks

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

metaworkssite

planits_itsclassifier

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

porteretal2019grid

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

porterhajibabaei2020_esvs_vs_otus

porterhajibabaei2021_pseudogene

Scripts and files to support the pseudogene manuscript.

rbcl_landplant_classifier

rbclclassifier

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

rbcldiatomclassifier

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

robinsonetal2020

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

robinsonetal2021_macroinvertdiatom

scvuiu_its_metabarcode_pipeline

Data flow to process ITS metabarcodes

scvur_16s_metabarcode_pipeline

Data flow to process 16S metabarcodes.

scvurl_rbcl_metabarcode_pipeline

Snakemake bioinformatic pipeline to process rbcL cp DNA metabarcodes

scvus_18s_metabarcode_pipeline

Data flow to process 18S rDNA metabarcodes

ssudiatomclassifier

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