.. GIP documentation master file, created by sphinx-quickstart on Mon Sep 14 10:59:47 2020. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. image:: _static/logo.jpg :width: 120px :alt: GIP logo :align: center 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`` .. figure:: _static/binCNV.multiPanel.png :width: 100 % Visualize SNV frequency together with sequencing depth in 3 isolates ``giptools SNV --samples LIPA83 ZK28 ZK5 --showCoverage`` .. figure:: _static/SNV.byChr_chr8.png :width: 100 % .. Compare gene CNVs in 3 specific isolates .. ``giptools ternary --gipOut gipOutDir --samples Lmj_A445 Lmj_1948 Ltr_16`` .. .. figure:: _static/triangle1.png .. :align: center .. :width: 500px .. `Gallery karyotype figure `_ 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 ------------ * `Singularity`_ 3.6.4 * `Nextflow`_ 20.10.0.5430 .. _Singularity: https://sylabs.io/guides/3.6/user-guide/quick_start.html#quick-installation-steps .. _Nextflow: https://www.nextflow.io 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 ---------- - Source Code: `https://github.com/giovannibussotti/GIP `_ - Discussions: `https://github.com/giovannibussotti/GIP/discussions `_ Support ------- If you are having issues, please let us know. - Issue Tracker: `https://github.com/giovannibussotti/GIP/issues `_ 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. Copyright --------- Copyright (c) 2021 Institut Pasteur .. toctree:: :maxdepth: 2 :hidden: software/index .. toctree:: :maxdepth: 2 :hidden: GIP/index .. toctree:: :maxdepth: 2 :hidden: giptools/index Indices and tables ================== * :ref:`genindex` * :ref:`search`