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AOML Omics Protocols

DOI

The repository contains protocols used by AOML Omics labs, made using the BeBOP-OBON protocol templates.

Protocols by category

Sample collection

DNA extraction

Metabarcoding (amplicon) library prep

Metagenomic (shotgun) library prep

Citing protocols

To cite the protocols here, refer to the version number in the individual protocol, e.g., "Water Sampling Protocol using Sterivex with Zirconia Beads v1.2.0". You can also cite the GitHub repository and the release number, e.g., "https://github.com/aomlomics/protocols 2024-11-26 Release" and/or the Zenodo archive of the release, e.g., "https://zenodo.org/records/14224755".

Protocol file formats

Markdown

The native format of the protcols is Markdown. Clicking on a protocol above will open the protocol in the folder markdown. To download the protocol, 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.

Word & HTML

For your convenience, we have generated Word and HTML versions of the protocols in the folders docx and html, respectively.

To generate alternate file formats from your Markdown protocol, follow the instructions below. This code is used in the script generate_docx_html.sh in this repository.

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 ../markdown/*.md. 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 commands pandoc "$output_file" --filter pandoc-mustache -o ../docx/"${input_file_base}.docx" and pandoc "$output_file" --filter pandoc-mustache -o ../html/"${input_file_base}.html" to generate the Word and HTML files, respectively.