Teresita M. Porter's repositories
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
12SfishClassifier
This repository contains 12S mitochondrial gene reference sets that can be used with the RDP Classifier to classify 12S metabarcode sequences from fish.
18SClassifier
This repository contains 18S reference sets that can be used with the RDP Classifier to classify 18S rDNA metabarcode sequences.
SCVUR_16S_metabarcode_pipeline
Data flow to process 16S metabarcodes.
rbcLClassifier
This repository contains rbcL reference sets that can be used with the RDP Classifier to classify rbcL metabarcode sequences.
SCVUIU_ITS_metabarcode_pipeline
Data flow to process ITS metabarcodes
SCVUS_18S_metabarcode_pipeline
Data flow to process 18S rDNA metabarcodes
UNITE_ITSClassifier
Fungal UNITE ITS reference set formatted for the Ribosomal Database Project (RDP) classifier.
Chronosequence
Supporting digital resources and scripts for the Porter et al., 2023 Sci Rep 13:7978 publication.
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
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).
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
PorterHajibabaei2021_pseudogene
Scripts and files to support the pseudogene manuscript.
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.
SCVURL_rbcL_metabarcode_pipeline
Snakemake bioinformatic pipeline to process rbcL cp DNA 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.