ADD: README.md: Documentation

README.md

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   <a href="https://coveralls.io/github/galantelab/sideRETRO?branch=master"><img alt="" src="https://coveralls.io/repos/github/galantelab/sideRETRO/badge.svg?branch=master" align="center"></a>
   <a href="https://hub.docker.com/r/galantelab/sider"><img alt="" src="https://img.shields.io/docker/cloud/build/galantelab/sider?color=blue" align="center"></a>
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+
+**sideRETRO** is a bioinformatic tool devoted for the detection of somatic (*de novo*) **retrocopy insertion**
+in whole genome and whole exome sequencing data (WGS, WES). The program has been written from scratch in C, and
+uses [HTSlib](http://www.htslib.org/) and [SQLite3](https://www.sqlite.org) libraries, in order to manage
+SAM/BAM reading and data analysis.
+
+## Functionalities
+
+When detecting retrocopies, **sideRETRO** can annotate several other features related to each event:
+
+* Parental gene
+
+   The gene which underwent retrotransposition process.
+
+* Host gene
+
+   It may happen that the retrotransposition event is inserted into another gene.
+
+* Genomic position
+
+   The genome coordinate where occurred the retrocopy integration event (chromosome:start-end).
+   It includes the insertion point (the expected exact point of each retrocopy insertion).
+
+* Strandness
+
+   Detects the orientation of the insertion (+/-). It takes into account the orientation of insertion,
+   whether in the leading (+) or lagging (-) DNA strand.
+
+* Genotype
+
+   When multiple individuals (genomes) are analyzed, **sideRETRO** discriminates events found in each one.
+   That way, it is possible to distinguish whether an event is exclusive or shared among the cohort analyzed.
+
+* Haplotype
+
+   Our tool provides information about the ploidy of the event, i.e., whether it occurs in one or both homologous
+   chromosomes (homozygous or heterozygous).
+
+## How it works
+
+**sideRETRO** compiles to an executable called `sider`, which has three subcommands: `process-sample`, `merge-call`
+and `make-vcf`. The `process-sample` subcommand processes a list of **SAM/BAM** files, and captures abnormal reads
+that must be related to an event of retrocopy. All those data is saved to a **SQLite3 database** and then we come
+to the second step `merge-call`, which processes the database and annotates all the retrocopies found. Finally we
+can run the subcommand `make-vcf` and generate a file (in **VCF** format) with retrocopies and further information
+about them. 
+
+## Installation
+
+The project depends on [Meson build system](https://mesonbuild.com) and [Ninja](https://github.com/ninja-build/ninja)
+to manage configuration and compilation process. They can be obtained using package manager or from source. For example,
+using [Ubuntu](https://ubuntu.com) distribution:
+
+```
+$ sudo apt-get install python3 \
+                       python3-pip \
+                       python3-setuptools \
+                       python3-wheel \
+                       ninja-build
+```
+
+and then:
+
+`$ pip3 install --user meson`
+
+Finally, clone this repository:
+
+`$ git clone https://github.com/galantelab/sideRETRO.git`
+
+Inside sideRETRO directory, run:
+
+`$ meson build && ninja -C build`
+
+You can find `sider` executable inside `build/src`. Optionally, install to system directories with:
+
+`$ sudo ninja -C build install`
+
+## Further reading
+
+For more details about installation, usage, examples and our methodology, please take a look at the
+online documentation: <https://sideretro.readthedocs.io>.
+
+## Acknowledgments
+
+- Coordination for the Improvement of Higher Level Personnel - [CAPES](http://www.capes.gov.br/)