# Scalable multi whole-genome alignment using recursive exact matching

## TL;DR

This paper introduces a new method for aligning multiple genomes efficiently and accurately, enabling better detection of genomic variations.

## Contribution

The novel recursive alignment approach with statistically supported decisions enables scalable whole-genome alignment.

## Key findings

- The method detects high-resolution structural variations between two human genomes.
- It produces high-quality multiple genome alignments for at least nineteen Mycobacterium tuberculosis genomes.

## Abstract

The emergence of third generation sequencing technologies has brought near perfect de-novo genome assembly within reach. This clears the way towards reference-free detection of genomic variations.

In this paper, we introduce a novel concept for aligning whole-genomes which allows the alignment of multiple genomes. Alignments are constructed in a recursive manner, in which alignment decisions are statistically supported. Computational performance is achieved by splitting an initial indexing data structure into a multitude of smaller indices.

We show that our method can be used to detect high resolution structural variations between two human genomes, and that it can be used to obtain a high quality multiple genome alignment of at least nineteen Mycobacterium tuberculosis genomes.

An implementation of the outlined algorithm called REVEAL is available on: https://github.com/jasperlinthorst/REVEAL