Reference Sequence Library Resources - Maine-eDNA

<p>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.</p> <p>These include:</p> <ul> <li> <p>RoughWorkflow.zip</p> </li> <ul> <li> <p>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)</p> </li> </ul> <li> <p>12S_REFDB.fasta</p> </li> <ul> <li> <p>A DADA2-compliant reference library for 12S sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list</p> </li> </ul> <li> <p>COI_REFDB.fasta</p> </li> <ul> <li> <p>A DADA2-compliant reference library for COI sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list</p> </li> </ul> <li> <p>GitHub Repo - referee - <a href="https://github.com/BigelowLab/referee">https://github.com/BigelowLab/referee</a></p> </li> <ul> <li> <p>Scripts for building reference databases for the Maine-eDNA project through downloading GenBank - this workflow is suggested especially for large species lists</p> </li> </ul> <li> <p>GitHub Repo - refdbtools - <a href="https://github.com/BigelowLab/refdbtools">https://github.com/BigelowLab/refdbtools</a>&nbsp;</p> </li> <ul> <li> <p>R language package to assist in making eDNA reference databases</p> </li> </ul> <li> <p>SpeciesListMeta_Shareable.xlsx</p> </li> <ul> <li> <p>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</p> </li> </ul> <li> <p>GNRMaineSpecies_May2024.csv</p> </li> <ul> <li> <p>A Maine (and surrounding area) species list ran through taxize&rsquo;s gnr_resolve to resolve species names and fill out taxonomy (full results)</p> </li> </ul> <li> <p>GNRMaineTaxonomiedSpecies_May2024.csv</p> </li> <ul> <li> <p>A Maine (and surrounding area) species list ran through taxize&rsquo;s gnr_resolve to resolve species names and fill out taxonomy (only species results that could be resolved with taxonomy)</p> </li> </ul> </ul> <p>&nbsp;</p> <p>Contact Beth Y. Davis - bethy.davis4@gmail.com for questions</p> <p>&nbsp;</p> <p>###</p> <p>Changelog:</p> <p>May 16, 2023 (Version 1.0) - Initial upload</p> <p>July 11, 2023 (Version 1.1) - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList</p> <p>May 20, 2024 (Version v3) -&nbsp; 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.</p> <p>November 27, 2024 (Version 4.0) - Updated Zenodo description and added the RoughWorkflow R files, 12S and COI files</p>