Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

Show full item record



Permalink

http://hdl.handle.net/10138/330375

Citation

Algorithms for Molecular Biology. 2021 May 25;16(1):6

Title: Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph
Author: Mukherjee, Kingshuk; Rossi, Massimiliano; Salmela, Leena; Boucher, Christina
Publisher: BioMed Central
Date: 2021-05-25
URI: http://hdl.handle.net/10138/330375
Abstract: Abstract Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran on E. coli. Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, rmapper is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper .
Subject: Optical mapping
Single molecule maps
de Bruijn graph
Overlap-layout-consensus
Genome assembly
Mis-assemblies
Rights: The Author(s)


Files in this item

Total number of downloads: Loading...

Files Size Format View
13015_2021_Article_182.pdf 2.381Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record