Skip to content

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal

License

Notifications You must be signed in to change notification settings

biocore/mg-scripts

Repository files navigation

# Sequence Processing Pipeline

A Jupyter notebook to assist wet lab shotgun pipeline. A packaged Python-based implementation of Knight Lab's sequencing process pipeline.

## Installation

To install this package, first clone this repository from GitHub:

`bash git clone https://github.com/biocore/mg-scripts.git `

Create a Python3 Conda environment in which to run the notebook:

`bash conda create -n sp_pipeline 'python==3.9' numpy pandas click scipy matplotlib fastq-pair `

Activate the Conda environment:

`bash source activate sp_pipeline `

Change directory to the cloned repository folder and install:

`bash cd mg-scripts pip install -e . `

This will automatically install https://github.com/biocore/metagenomics_pooling_notebook.git, a dependency of mg-scripts and the sequence_processing_pipeline.

## Running Unittests

Change directory to the downloaded repository folder:

`bash cd mg-scripts nosetests --with-coverage --cover-inclusive --cover-package sequence_processing_pipeline `

## Getting Started

Review Pipeline.py and main.py to learn how to import and access package functionality:

`bash cd mg-scripts/sequence_processing_pipeline more Pipeline.py more main.py `

Adjust configuration settings as needed:

`bash cd mg-scripts/sequence_processing_pipeline vi configuration.json `

Please note that the setting 'minimap2_databases' is expected to be a list of paths to individual .mmi files for QCJob. For NuQCJob, minimap2_databases is expected to be the path to a directory containing two subdirectories: 'metagenomic' and 'metatranscriptomic'. Each directory should contain or symlink to the appropriate .mmi files needed for that Assay type.

About

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published