Scripts and additional material for the manuscript: ITS1 Metabarcoding highlights the low specificity of lichen mycobiomes at a local scale.
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Updated
May 22, 2017 - TeX
Scripts and additional material for the manuscript: ITS1 Metabarcoding highlights the low specificity of lichen mycobiomes at a local scale.
Repository for ITS diagnostics development as part of Phytothreats project
COI sequences files used to test the COI Classifier Web Portal
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).
Trimming Sanger sequencing reads by quality
Data processing workflow and supplementary data for Li et al. 2019 - Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
Datasets and code used to create figures in "Hajibabaei et al., 2019. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14(9): e0220953."
Datasets and code used to create figures in "Hajibabaei et al., 2019. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS ONE 14(12): e0225409."
Supplementary files for Ribeiro et al. ISME 2018
Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
Public repository of data and analyses from Dirks and Jackson (2020), "Community structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy", Applied and Environmental Microbiology 86 (19)
Data flow to process COI metabarcodes
Snakemake bioinformatic pipeline to process COI mtDNA metabarcodes
Simulator of metabarcoding sequencing runs - Glorified ART wrapper
Code and plots for the paper of Jauss & Walden et al., 2020, https://www.frontiersin.org/articles/10.3389/fmicb.2020.592189/
A collection of singularity recipies for bioinformatic pipelines.
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