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<p align="center"><a href="https://sideretro.readthedocs.io/en/latest/?badge=latest"><img src="docs/images/logo_sideRETRO.png" alt="sideRETRO" width="200"></a></p>
<h2 align="center">A pipeline for detecting Somatic Insertion of DE novo RETROcopies</h2>
<p align="center">
<a href="https://github.com/galantelab/sideRETRO/actions/workflows/ci.yml"><img alt="" src="https://github.com/galantelab/sideRETRO/actions/workflows/ci.yml/badge.svg?branch=master" align="center"></a>
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<a href="https://sideretro.readthedocs.io/en/latest/?badge=latest"><img alt="" src="https://readthedocs.org/projects/sideretro/badge/?version=latest" align="center"></a>
<a href="https://github.com/galantelab/sideRETRO/tags/"><img src="https://img.shields.io/github/tag/galantelab/sideRETRO?include_prereleases=&sort=semver&color=blue" alt="GitHub tag" align="center"></a>
<a href="https://hub.docker.com/r/galantelab/sider/tags"><img alt="" src="https://img.shields.io/badge/docker-%230db7ed.svg?style=flat&logo=docker&logoColor=white" align="center"></a>
</p>
**sideRETRO** is a bioinformatic tool devoted for the detection of somatic **retrocopy** insertion, also known as
**retroCNV**, 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/CRAM** reading and data analysis.
For full documentation, please visit <https://sideretro.readthedocs.io>.
### Features
When detecting retrocopies, **sideRETRO** can annotate several other features related to each event:
* **Parental gene**
The gene which underwent retrotransposition process.
* **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.
* **Genomic context**
The retrocopy integration site context: If the retrotransposition event occurred at an intergenic or
intragenic region - the latter can be splitted into exonic and intronic according to the host gene.
* **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).
## Getting Started
### 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`
(or: `$ sudo apt install 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`
### Usage
**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/CRAM** 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.
```sh
# List of BAM files
$ cat 'my-bam-list.txt'
/path/to/file1.bam
/path/to/file2.bam
/path/to/file3.bam
# Run process-sample step
$ sider process-sample \
--annotation-file='my-annotation.gtf' \
--input-file='my-bam-list.txt'
$ ls -1
my-genome.fa
my-annotation.gtf
my-bam-list.txt
out.db
# Run merge-call step
$ sider merge-call --in-place out.db
# Run make-vcf step
$ sider make-vcf \
--reference-file='my-genome.fa' out.db
```
## Citation
If sideRETRO was somehow useful in your research, please cite it:
```bib
@article{10.1093/bioinformatics/btaa689,
author = {Miller, Thiago L A and Orpinelli, Fernanda and Buzzo, José Leonel L and Galante, Pedro A F},
title = "{sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies}",
journal = {Bioinformatics},
year = {2020},
month = {07},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btaa689},
url = {https://doi.org/10.1093/bioinformatics/btaa689},
note = {btaa689},
}
```
## License
This is free software, licensed under:
`The GNU General Public License, Version 3, June 2007`
|
