Rala

Layout module for raw de novo DNA assembly of long uncorrected reads.

Description

Rala is intended as a standalone layout module to assemble raw reads generated by third generation sequencing. It trims sequence adapters, purges chimeric sequences and removes repeat-induced overlaps by examining sequence pile-o-gram. Afterwards, an assembly graph is built and simplified in the default way, i.e. applied are transitive reduction, tipping and bubble popping. Leftover tangles are resolved by laying out the graph in a 2D plane with the help of the force directed placement algorithm, and long edges are removed (see figures bellow).

Rala takes as input two files: sequences in FASTA/FASTQ format and overlaps between them in PAF/MHAP format. Both input files can be compressed with gzip. Output is a set of contigs in FASTA format.

For maximal performance, Rala should be run twice with minimap (or minimap2) to improve repeat annotation due to k-mer filtering. A sample run can be seen bellow (and found in misc/raven.sh alongside minimap2 version):

minimap -t <threads> -L100 -Sw5 -m0 <sequences> <sequences> > overlaps.paf

rala -t <threads> -p <sequences> overlaps.paf > uncontained.fasta

minimap -t <threads> -L100 -w5 -m0 -f0.00001 uncontained.fasta <sequences> > uncontained.paf

rala -t <threads> -s uncontained.paf <sequences> overlaps.paf > <layout>

Pile-o-gram of a chimeric read

Pile-o-gram of two reads which overlap on a repetitive region

Force directed layout of an assembly graph with highlighted false overlaps&

Dependencies

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

Installation

To install Rala run to following commands:

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

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

Optionally, you can run sudo make install to install rala executable to your machine.

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

Usage

Usage of rala is as following:

rala [options ...] <sequences> <overlaps>

    <sequences>
        input file in FASTA/FASTQ format (can be compressed with gzip)
        containing sequences
    <overlaps>
        input file in MHAP/PAF format (can be compressed with gzip)
        containing pairwise overlaps

    options:
        -p, --preconstruct
            print uncontained sequences for second iteration
        -s, --sensitive-overlaps <file>
            input file in MHAP/PAF format (can be compress with gzip)
            containing more sensitive overlaps
        -u, --include-unassembled
            output unassembled sequences (singletons and short contigs)
        -d, --debug <string>
            enable debug output with given prefix
        -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.