# Ra

**Repository Path**: scnet-lib/ra

## Basic Information

- **Project Name**: Ra
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2023-10-24
- **Last Updated**: 2023-10-24

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Ra

[![Build status for c++/clang++](https://travis-ci.org/rvaser/ra.svg?branch=master)](https://travis-ci.org/rvaser/ra)

Overlap-layout-consensus based DNA assembler of long uncorrected reads (short for Rapid Assembler).

## Description

Ra is as a fast and easy to use assembler for raw reads generated by third generation sequencing. It consists of [Minimap2](https://github.com/lh3/minimap2), [Rala](https://github.com/rvaser/rala) and [Racon](https://github.com/isovic/racon) as depicted on figure bellow.

Ra takes as input a single file containing raw reads in FASTA/FASTQ format (can be compressed with gzip) and outputs a set of contigs with high accuracy in FASTA format to stdout. Additionally, a file containing second generation sequences in FASTA/FASTQ format (can be compressed with gzip) can be passed as second argument in order to polish the final assembly.

*Ra flow chart*
![](misc/ra_components.png)

## Dependencies
1. gcc 4.8+ or clang 3.4+
2. cmake 3.2+

## Installation
To install Ra run to following commands:

```bash
git clone --recursive https://github.com/rvaser/ra.git ra
cd ra
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
```

After successful installation, an executable named `ra` will appear in `build/bin`.

***Note***: if you omitted `--recursive` from `git clone`, run `git submodule update --init --recursive` before proceeding with compilation.

## Usage

Usage of ra is as following:

    ra [options ...] -x {ont, pb} <sequences> [<ngs_sequences>]

        <sequences>
            input file in FASTA/FASTQ format (can be compressed with gzip)
            containing third generation sequencing reads
        <ngs_sequences>
            input file in FASTA/FASTQ format (can be compressed with gzip)
            containing next generation sequencing reads

        required arguments:
            -x {ont, pb}
                sequencing technology of input sequences

        options:
            -t, --threads <int>
                default: 1
                number of threads
            --version
                prints the version number
            -h, --help
                prints the usage

## Contact information

For additional information, help and bug reports please send an email to: robert.vaser@fer.hr.

## Acknowledgement

This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353.