A hierarchical network heuristic for solving the orientation problem in genome assembly

TL;DR

This paper introduces a hierarchical clustering algorithm that robustly solves the orientation problem in genome assembly, effectively handling errors and noise in both simulated and real bacterial data.

Contribution

The paper presents a novel hierarchical clustering-based method for genome assembly orientation that improves robustness against errors and noise compared to existing algorithms.

Findings

Successfully solves orientation problem in simulated data

Accurately orients contigs in real R. sphaeroides data

Demonstrates stability to data errors and initial conditions

Abstract

In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves building ordered and oriented linear collections of contigs (continuous overlapping sequence reads) called scaffolds and relies on the use of mate pair data. A mate pair is a set of two reads that are sequenced from the ends of a single fragment of DNA, and therefore have opposite mutual orientations. When two reads of a mate-pair are placed into two different contigs, one can infer the mutual orientation of these contigs. While several orientation algorithms exist as part of assembly programs, all encounter challenges while solving the orientation problem due to errors from mis-assemblies in contigs or errors in read placements. In this paper we present an algorithm based on hierarchical clustering that independently solves the orientation problem and is robust to errors. We show that our algorithm can correctly solve the orientation problem for both faux (generated) assembly data and real assembly data for {\em R. sphaeroides bacteria}. We demonstrate that our algorithm is stable to both changes in the initial orientations as well as noise in the data, making it advantageous compared to traditional approaches.