MitoPilot
An R package for scalable mitogenome assembly and annotation, uses Nexflow and includes (Shiny) web app for project management and curation of results. Currently supports fish and starfish datasets, but will be expanded to other taxa soon. Developed as a joint effort by the NOAA National Systematics Lab and the Smithsonian Ocean DNA Initiative
rCRUX Reference Database Generating Tool
This R package generates reference databases for eDNA metabarcoding from user-supplied primer sequences. The package employs iterative Basic Alignment Search Tool (BLAST) searches paired with quality control to produce a final reference library.
Mitohelper
This Python-based tool is designed to assist with preparing eDNA reference databases for fishes. It can determine whether a reference sequence exists for a specific species/group and visualize the available sequenced regions of target genes.
Tourmaline metabarcoding pipeline
Detailed Snakemake workflow for standardized, repeatable processing and classifying of eDNA sequence data. Uses the popular QIIME 2 software
Anacapa metabarcoding pipeline
eDNA toolkit to build reference databases, assign taxonomy, and explore biodiversity statistics. Works for a variety of markers, including 12S, 16S, 18S, ITS2, and CO1.
SEDNA Workflows
List of scripts, pipelines, and tools for a variety of analyses including whole genome sequencing workflows, SNP discovery, microhaplotype genotyping, population assignment, historical demography. All written specifically for the NOAA NMFS SEDNA bioinformatics computing cluster.