Skip to content

NOAA-PMEL/Ocean-Molecular-Ecology

Repository files navigation

NOAA PMEL Ocean Molecular Ecology Group

Home for NOAA Pacific Marine Environmental Laboratory Ocean Molecular Ecology group bioinformatics and data analysis.

Authors

Zachary Gold
Sean McAllister
Shannon Brown
Han Weinrich
Sam Setta
Brynn Zalmanek

Zenodo Archive

NOAA/PMEL Ocean Molecular Ecology Zenodo Community

Protocols

eDNA Sample Collection Protocols

Type
eDNA Collection with Sterviex and Peristaltic Pump
eDNA Collection with Sterviex and Gravity Bag
eDNA Collection with Smith-Root Self Preserving eDNA Filter and Persitaltic Pump
eDNA Collection with Disc Filtration with a Vacuum Pump

Organismal Sample Collection Protocols

Type
Organismal Subsampling and Tissue Extraction Protocol

Extraction Protocols

Type
eDNA Sterivex Extraction Proctocol
eDNA Disc Filter Extraction Protocol

DNA Quantification Protocols

Type
Qubit Quantification Protocol

PCR Protocols

Marker
Parada universal 16S
Stoeck phytoplankton 18S V4
AmaralZettler phytoplankton 18S V9
MiFish modified Universal Teleost 12S
LF metazoan COI
Baker marine mammal dLoop
Kelly Metazoan 16S
White Sterling Phytoplankton ITS1
Machida Metazoan 18S V8

PCR Quantification Protocols

Type
Gel Electrophoresis Protocol

qPCR Protocols

Marker
Metacarcinus magister nad2 v1

Bioinformatics & Data Analysis Repositories

Metabarcoding Pipeline and Visualization software - REVAMP
Reference Database Generating Tool - rCRUX

Data Management

NOAA 'Omics Draft Data Management Guidelines
How To Make A BeBOP Protocol.pdf

Suggested Links

Manuscripts

Gold et al. 2023 Code - Ichthyoplankton from CalCOFI Ethanol Preservative
Gold et al. 2023 Code - Signal and Noise from Metabarcoding data

NOAA Collaborators

AOML 'Omics GitHub
GLERL Github
CalCOFI Github
West Coast Ocean Biomolecular Observation Network

Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

About

Main repository for NOAA Pacific Marine Environmental Laboratory Ocean Molecular Ecology group bioinformatics and data analysis.

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

 
 
 

Contributors

Languages