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-# XAVIER - e**X**ome **A**nalysis and **V**ariant explor**ER** 🔬
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-[![tests](https://github.com/CCBR/XAVIER/workflows/tests/badge.svg)](https://github.com/CCBR/XAVIER/actions/workflows/main.yaml)
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-[![GitHub Issues](https://img.shields.io/github/issues/CCBR/XAVIER?color=brightgreen)](https://github.com/CCBR/XAVIER/issues)
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-> **_XAVIER - eXome Analysis and Variant explorER_**. **XAVIER** is an open-source, reproducible, and scalable solution for analyzing Whole Exome sequencing data. Its long-term goals: to accurately call germline and somatic variants, to infer CNVs, and to boldly annotate variants like no pipeline before!
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-## Overview
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-Welcome to XAVIER's documentation! This guide is the main source of documentation for users that are getting started with the [XAVIER pipeline](https://github.com/CCBR/XAVIER).
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-The **`xavier`** 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:
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-- [<code>xavier <b>run</b></code>](usage/run.md): Run the XAVIER pipeline with your input files.
-- [<code>xavier <b>unlock</b></code>](usage/unlock.md): Unlocks a previous runs output directory.
-- [<code>xavier <b>cache</b></code>](usage/cache.md): Cache remote resources locally, coming soon!
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-XAVIER is a comprehensive whole exome-sequencing pipeline following the Broad's set of best practices. It relies on technologies like [Singularity<sup>1</sup>](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake<sup>2</sup>](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster or cloud provider.
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-The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ or BAM files and can be run locally on a compute instance, on-premise using a cluster, or on the cloud (feature coming soon!). A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM, or run on AWS using Tibanna (feature coming soon!). A hybrid approach ensures the pipeline is accessible to all users.
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-Before getting started, we highly recommend reading through the [usage](usage/run.md) section of each available sub command.
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-For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/CCBR/XAVIER/issues).
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-## Contribute
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-This site is a living document, created for and by members like you. XAVIER is maintained by the members of CCBR and is improved by continuous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/CCBR/XAVIER/).
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-## References
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-<sup>**1.** Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.</sup>  
-<sup>**2.** Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>
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