43 0

The present and future of de novo whole-genome assembly

Title
The present and future of de novo whole-genome assembly
Author
남진우
Keywords
de novo assembly algorithms; de Bruijn graph; next-generation sequencing; single-molecule sequencing
Issue Date
2018-01
Publisher
OXFORD UNIV PRESS
Citation
BRIEFINGS IN BIOINFORMATICS, v. 19, no. 1, page. 23-40
Abstract
As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome.
URI
https://academic.oup.com/bib/article-abstract/19/1/23/2339783?redirectedFrom=fulltexthttps://repository.hanyang.ac.kr/handle/20.500.11754/117136
ISSN
1467-5463; 1477-4054
DOI
10.1093/bib/bbw096
Appears in Collections:
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
Files in This Item:
There are no files associated with this item.
Export
RIS (EndNote)
XLS (Excel)
XML


qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

BROWSE