Genome Instability Pipeline

The Genome Instability Pipeline (GIP) will solve your problem of analyzing whole genome sequencing (WGS) data making bioinformatics screenings faster and easier.
GIP allows the batch processing of multiple WGS experiments, including the mapping of short reads, the quantification of chromosomes, genes and genomic bins.
The results of GIP are summarized in a report page providing sequencing experiment and mapping statistics, graphical representations of genomic features quantifications, and excel tables.

GIP also enables giptools, a tool-suite allowing to Detect, Compare and Visualize

  • Aneuploidy changes

  • Gene copy number variants (CNVs)

  • Single nucleotide variants (SNVs)

  • Structural variants (SVs)

Look how easy it is to use.

Run GIP on a large set of input WGS experiments (e.g. 200 samples)

gip --genome fasta.file --annotation gtf.file --index fastqs.tsv -c gip.config

Compare the genomic bin CNVs in 2 specific isolates

giptools binCNV --samples ZK43 LIPA83

_images/binCNV.multiPanel.png

Visualize SNV frequency together with sequencing depth in 3 isolates

giptools SNV --samples LIPA83 ZK28 ZK5 --showCoverage

_images/SNV.byChr_chr8.png

Features

  • Scalable workflow implemented in Nextflow

  • Reproducible thanks to the Singularity support

  • Easy-to-use and easy-to-install

  • Support for multi-copy gene clusters

  • Custom comparison of samples sub-sets

  • Publication quality figures and excel tables

  • Generally applicable both to model and non-model species

Requirements

These are the specific versions that were tested. Use other versions at your own risk.

Installation

  1. Download GIP

    git clone https://github.com/giovannibussotti/GIP.git

  2. Pull the container

    singularity pull giptools library://giovannibussotti/default/giptools

  3. Move giptools to /usr/local/bin/. If the user does not have permission on the folder she/he can keep giptools in any other location, and just update the “container” parameter in the gip.config: container='/Path/To/giptools'

Done!
To make GIP available anywhere, the user can place gip in a directory that is in PATH.

Contribute

Support

If you are having issues, please let us know.

License

GIP and giptools are free software licensed under the GNU General Public License version 3. Third parties software and scripts installed in giptools have their own copyright and license. A list is provided in the next page of this documentation. Users of gip and giptools must take notice and agree with the terms and conditions of all third party software.

Indices and tables