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bioinformatics-illuminamgi

SOPs or documents related to Illumina/MGI sequencing bioinformatics pipeline

https://github.com/monashowl/bioinformatics-illuminamgi

Science Score: 44.0%

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Repository

SOPs or documents related to Illumina/MGI sequencing bioinformatics pipeline

Basic Info
  • Host: GitHub
  • Owner: MonashOWL
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 5.7 MB
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  • Watchers: 1
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Created almost 2 years ago · Last pushed 8 months ago
Metadata Files
Readme Citation

README.md

Bioinformatics-IlluminaMGI

SOPs or documents related to Illumina/MGI sequencing bioinformatics pipeline.

The bioinformatics SOPs written over here assumes that you already have access to Monash MASSIVE account and project (https://www.massive.org.au/index.html). If you use other cluster computing systems (or do not have access to one), please feel free to modify the script to suit yours.

For the guidelines, I wrote the script based on my MASSIVE account, project, and directory, so please modify the codes as per yours.

In terms of directory within the scripts, I will be replacing the project folder directory (e.g., /fs04/hj18/) with ~/ to avoid confusion. You can name your directory based on your preference, it will not cause any issue with running of scripts.

**16S sequencing**

You can start off by looking at the following documentations: 1) Setting up WINSCP and PUTTY (WINSCP and PUTTY setup22032024.docx) 2) FIGARO and FASTP setup (FIGARO and FASTP setup15032024.docx) - located in 16S folder 3) Illumina sequencing pipeline (Illumina sequence pipeline30062025.docx) - located in 16S folder 4) Leave one out, LOO (Leave one out at a time (LOO) pipeline17032024.docx) - located in 16S folder (note that there is a demo folder and Jupyter notebook to better visualise the process) 5) Source variability, i.e., assessing source library based on number of included source samples (Source variability pipeline30102024.docx_) - located in 16S folder (note that there is a demo folder and Jupyter notebook to better visualise the process)

For these pipeline, at minimum you would need to have Python (for LOO (4) and source variability (5)) (https://www.python.org/), QIIME2 (https://qiime2.org/) and SourceTracker (https://github.com/caporaso-lab/sourcetracker2). These software are freely available to be used.

For any questions, please feel free to email me at timothy.lim@monash.edu, or contact OneWater Laboratory at onewater@monash.edu.

Owner

  • Name: Monash One Water Lab
  • Login: MonashOWL
  • Kind: organization
  • Email: onewater@monash.edu

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Bioinformatics-IlluminaMGI
message: >-
  If you use this dataset, please cite it using the metadata
  from this file.
type: dataset
authors:
  - given-names: Timothy Jia-Young
    family-names: Lim
    email: timothy.lim@monash.edu
    affiliation: Monash University
    orcid: 'https://orcid.org/0000-0002-8798-4895'
repository-code: >-
  https://github.com/MonashOWL/Bioinformatics-IlluminaMGI/
url: 'https://github.com/MonashOWL/Bioinformatics-IlluminaMGI'
version: '17032024'
date-released: '2024-03-17'

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