Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements.

Burkhard Morgenstern,Armando J Pinho,Diogo Pratas,Morteza Hosseini

doi:10.1093/gigascience/giaa048

Burkhard Morgenstern, Armando J Pinho + Show 2 more

Open Access

https://doi.org/10.1093/gigascience/giaa048

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Abstract

BackgroundThe development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer.ResultsWe present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image.ConclusionsTested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ∼1 GB, which makes Smash++ feasible to run on present-day standard computers.

Highlights

The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery
We present Smash++, an alignment-free tool that finds chromosomal rearrangements between two DNA sequences based on their information content, which is obtained by a data compression technique
Finding genomic rearrangements is crucial, since they play an important role in genetic disorders, cancer and chromosomal evolution

Summary

Introduction

The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial due to their role in chromosomal evolution, genetic disorders and cancer; Results: We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between two DNA sequences. This computational solution extracts information contents of the two sequences, exploiting a data compression technique, in order for finding rearrangements. With the ever-increasing development of high-throughput sequencing (HTS) technologies, a massive amount of genomic information is produced at much higher speed and lower cost than was possible before [1].

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