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README.md

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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 in the pipelines directory.

Publication

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.

Getting started

To run PiGx on your experimental data, describe your samples in a CSV file 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 pigx --help.

Install

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 --enable-PIPELINE and --disable-PIPELINE arguments to the configure script. PIPELINE is one of bsseq, rnaseq, scrnaseq, chipseq, and crispr. For more options run ./configure --help.

License

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.

See LICENSE for the full license text.