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ioos / bio_data_guide

Standardizing Marine Biological Data Working Group - An open community to facilitate the mobilization of biological data to OBIS.
https://ioos.github.io/bio_data_guide/
MIT License
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Fish 16S microbiome reads #199

Open lardinois21 opened 5 months ago

lardinois21 commented 5 months ago

Contact details

laura.lardinois@mail.mcgill.ca

Dataset Title

Fish Microbiome 16S 2021-22

Describe your dataset and any specific challenges or blockers you have or anticipate.

I have several sets of fish skin and gut 16S microbiome datasets, which are paired with large metadata files on each individual. I'd like to start making these data compatible with the Darwin Core framework to be able to share them, and find ways to optimize our metadata collection and organization to be able to minimize the amount of data cleaning and re-formatting needed for future samples. Challenges: metadata needs ReadME file to explain site names and abbreviations, sheer volume of sequencing reads exceeds laptop memory.

Info about "raw" Data Files.

metadata: .csv file, raw reads = .fastq files (or .fastq gz - compressed)

github-actions[bot] commented 2 months ago

Thank you for identifying this dataset for mobilization. The workshop hosts wanted to check in. Is there anything you need help with in order to mobilize this dataset to OBIS? If you would like assistance from an OBIS node you can find node contacts listed here.