Reference Sequence Library Resources - Maine-eDNA

The following files and resources are associated with the Maine-eDNA Reference Library Research Group - aiming to create reference sequence library resources for researchers part of Maine-eDNA or otherwise interested in leveraging eDNA tools for research in the Gulf of Maine.

These include:

RoughWorkflow.zip

contains a NCBI scraping script to build reference databases based on an input species list, a configuration file for the script, and genbankr version - most useful for shorter species lists (time-intensive)

12S_REFDB.fasta

A DADA2-compliant reference library for 12S sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list

COI_REFDB.fasta

A DADA2-compliant reference library for COI sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list

GitHub Repo - referee - https://github.com/BigelowLab/referee

Scripts for building reference databases for the Maine-eDNA project through downloading GenBank - this workflow is suggested especially for large species lists

GitHub Repo - refdbtools - https://github.com/BigelowLab/refdbtools 

R language package to assist in making eDNA reference databases

SpeciesListMeta_Shareable.xlsx

Describes the sources from which the GNRMaineSpecies_May2024.csv and GNRMaineTaxonomiedSpecies_May2024.csv species lists were compiled - sources not associated with a link were found as separate files and are hosted elsewhere. Species list sources are courtesy of public datasets, Maine-eDNA researchers, and collaborators

GNRMaineSpecies_May2024.csv

A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (full results)

GNRMaineTaxonomiedSpecies_May2024.csv

A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (only species results that could be resolved with taxonomy)

Contact Beth Y. Davis - [e-mail] for questions

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Changelog:

May 16, 2023 (Version 1.0) - Initial upload

July 11, 2023 (Version 1.1) - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList

May 20, 2024 (Version v3) -  Additional cleaning to correct deduplication errors and ran taxize's gnr_resolve to resolve names and fill out taxonomy. The version update adds two files, GNRMaineSpecies_May2024.csv containing the full result of gnr_resolve, and GNRMaineTaxonomiedSpecies_May2024.csv contains only those species from the original list that could be resolved with taxonomy. The SpeciesListMeta_Shareable.csv has not been updated but is still an accurate tracker of the sources from which the species names were gained from.

November 27, 2024 (Version 4.0) - Updated Zenodo description and added the RoughWorkflow R files, 12S and COI files