mutation-seek 🔬

An awesome quantitative genetics pipeline

This is the home of the pipeline, mutation-seek. Its long-term goals: to boldly detect physiological homogeneity within genetic heterogeneity and to perform error-prone data preparation for genome-wide association studies (GWAS) like no pipeline before!

Overview¶

Welcome to mutation-seek's documentation! This guide is the main source of documentation for users that are getting started with the long pipeline name.

The ./mutation-seek pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

mutation-seek run
Run the mutation-seek pipeline with your input files.

mutation-seek unlock
Unlocks a previous runs output directory.

mutation-seek install
Download remote reference files locally.

mutation-seek cache
Cache remote software containers locally.

mutation-seek is a comprehensive pipeline for quantitative genetics. It relies on technologies like Singularity¹ to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake², a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the usage section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github.

Contribute¶

This site is a living document, created for and by members like you. mutation-seek is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository .

Citation¶

If you use this software, please cite it as below:

BibTexAPA

Citation coming soon!

Citation coming soon!

References¶

^{1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.}
^{2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.}

Last update: 2024-09-19