Optical map guided genome assembly

Miika Leinonen,Leena Salmela

doi:10.1186/s12859-020-03623-1

Miika Leinonen, Leena Salmela

Open Access

https://doi.org/10.1186/s12859-020-03623-1

Copy DOI

Abstract

BackgroundThe long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly.ResultsWe propose OpticalKermit which directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler, OpticalKermit produces an assembly with almost three times higher NGA50 with a lower number of misassemblies on real A. thaliana reads.ConclusionsOpticalKermit successfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.

Highlights

The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced
The long reads produced by third generation sequencing technologies such as Pacific Biosciences and Oxford Nanopore have enabled large improvements in de novo genome assembly
We concentrate on using optical mapping data to improve genome assembly

Summary

Introduction

The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Assemblies produced solely on read data are not complete and typically contain orders of magnitudes more contigs than the sequenced organism has chromosomes To further improve these assemblies, several long-range technologies such as optical mapping, genetic linkage maps, and Hi-C based analysis have been developed [1]. A restriction enzyme which cuts at a specific DNA motif is applied on the DNA molecules and the order and Leinonen and Salmela BMC Bioinformatics (2020) 21:285 length of the resulting fragments are measured by imaging [2, 3]. This results in raw optical mapping data which is assembled to genome-wide optical maps

Objectives

Methods

Results

Discussion

Conclusion