What is PiGx?
PiGx is a collection of genomics pipelines. More information can be found in PiGx website
It includes the following pipelines:
PiGx BSseq for raw fastq read data of bisulfite experiments
PiGx RNAseq for RNAseq samples
PiGx scRNAseq for single cell dropseq analysis
PiGx ChIPseq for reads from ChIPseq experiments
PiGx CRISPR (work in progress) for the analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data
All pipelines are easily configured with a sample sheet (in CSV
format) and a descriptive settings file (in YAML format). For more
detailed information see the README.md file for each of the pipelines
Wurmus R, Uyar B, Osberg B, Franke V, Gosdschan A, Wreczycka K, Ronen J, Akalin A. PiGx: Reproducible genomics analysis pipelines with GNU Guix. Gigascience. 2018 Oct 2. doi: 10.1093/gigascience/giy123. PubMed PMID: 30277498.
To run PiGx on your experimental data, describe your samples in a CSV
sample_sheet.csv, provide a
settings.yaml to override the
defaults defaults, and select the pipeline.
To generate a settings file template for any pipeline:
pigx [pipeline] --init=settings
To generate a sample sheet template for any pipeline:
pigx [pipeline] --init=sample-sheet
Here's a simple example to run the RNAseq pipeline:
pigx rnaseq my-sample-sheet.csv --settings my-settings.yaml
To see all available options run
Pre-built binaries for PiGx are available through GNU Guix, the functional package manager for reproducible, user-controlled software management. Install the complete pipeline bundle with the following command:
guix install pigx
If you want to install PiGx from source, please make sure that all required dependencies are installed and then follow the common GNU build system steps after unpacking the latest release tarball:
./configure --prefix=/some/where make install
You can enable or disable each of the pipelines with the
--disable-PIPELINE arguments to the
PIPELINE is one of
crispr. For more options run
All PiGx pipelines are free software: you can redistribute PiGx and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
LICENSE for the full license text.