README.md

AOML 'Omics Protocols

Protocols used by AOML 'Omics labs, made using the BeBOP-OBON protocol templates.

Each protocol has its own repository (listed below) and can be referenced using its own Zenodo DOI (with versioning).

Legacy references to this repository should be changed.

Protocols by category

Sample collection

• https://github.com/aomlomics/protocol_sampling_sterivex_beads
• https://github.com/aomlomics/protocol_sampling_sterivex_dry

DNA extraction

• https://github.com/aomlomics/protocol_extract_dna_sterivex_kingfisher
• https://github.com/aomlomics/protocol_extract_dna_sedtrap_powersoil

Metabarcoding (amplicon) library prep

• https://github.com/aomlomics/protocol_pcr_ssu16sv4v5_emp
• https://github.com/aomlomics/protocol_pcr_ssu18sv9_emp
• https://github.com/aomlomics/protocol_pcr_ssu12sv5v6_mifish

Metagenomic (shotgun) library prep

• https://github.com/aomlomics/protocol_libprep_metag_illumina

Citing protocols

To cite the protocols here, go to the protocol's repository and copy the Zenodo link provided there. If there are multiple releases (versions), be sure to cite the DOI associated with the release you are using.

Protocol file formats

Markdown

The native format of the protcols is Markdown. To download a protocol, go to that protocol's repsitory, click on the file name, and click on the "Download raw file" button on the right side of the tool bar above the document. To view and/or print the protocol, open the Markdown file in a Markdown editor such as Typora or Visual Studio Code.

Other formats

To generate alternate file formats from a Markdown file -- for example, Word, HTML, or PDF -- follow the instructions below.

Install

Create a conda environment called writing and install pandoc and pandoc-mustache:

conda create --name writing pip
conda activate writing
conda install -c conda-forge pandoc
pip install -U pandoc-mustache

Run

From the code directory, run the command ./pandoc.sh path/to/markdown/*.md, where "path/to/markdown" is a directory containing one or more Markdown protocols you want to convert. This script does the following for each Markdown file:

• Create a file called mustache.yaml with all the YAML terms from the frontmatter.
• Replace the YAML frontmatter with a single line mustache: mustache.yaml in the Markdown document mustache.yaml. Note: Only YAML terms in this separate YAML file will be readable. Other YAML frontmatter in the Markdown document is ignored by pandoc.
• Run pandoc with the command pandoc protocol.md --filter pandoc-mustache -o protocol.docx to generate the Word file. Change "docx" to "html" or "pdf to generate HTML and PDF files, respectively.

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.