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, Rala and 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

Dependencies

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

Installation

To install Ra run to following commands:

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.