Optimal hybrid sequencing and assembly: Feasibility conditions for accurate genome reconstruction and cost minimization strategy

Computational Biology and Chemistry
Chun-Chi ChenByung-Jun Yoon

Abstract

Recent advances in high-throughput genome sequencing technologies have enabled the systematic study of various genomes by making whole genome sequencing affordable. Modern sequencers generate a huge number of small sequence fragments called reads, where the read length and the per-base sequencing cost depend on the technology used. To date, many hybrid genome assembly algorithms have been developed that can take reads from multiple read sources to reconstruct the original genome. However, rigorous investigation of the feasibility conditions for complete genome reconstruction and the optimal sequencing strategy for minimizing the sequencing cost has been conspicuously missing. An important aspect of hybrid sequencing and assembly is that the feasibility conditions for genome reconstruction can be satisfied by different combinations of the available read sources, opening up the possibility of optimally combining the sources to minimize the sequencing cost while ensuring accurate genome reconstruction. In this paper, we derive the conditions for whole genome reconstruction from multiple read sources at a given confidence level and also introduce the optimal strategy for combining reads from different sources to minimize the overal...Continue Reading

References

Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R M Idury, M S Waterman
Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·P A PevznerM S Waterman
Jun 15, 2007·Heredity·I J Leitch
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Oct 28, 2008·Bioinformatics·Jason R MillerGranger Sutton
Mar 10, 2010·Genomics·Jason R MillerGranger Sutton
May 21, 2010·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Martin Kircher, Janet Kelso
Sep 14, 2010·Bioinformatics·Xiao YangSrinivas Aluru
Oct 27, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xiaohong ZhaoGayle M Wittenberg
Dec 1, 2010·Bioinformatics·Lucian IlieSilvana Ilie
May 27, 2011·Analytical Chemistry·Thomas P NiedringhausAnnelise E Barron
Nov 10, 2011·Nature Biotechnology·Phillip E C CompeauGlenn Tesler
Dec 8, 2011·Genome Research·Steven L SalzbergJames A Yorke
Apr 12, 2012·Briefings in Bioinformatics·Xiao YangSrinivas Aluru
Jul 4, 2012·Nature Biotechnology·Ali BashirEric E Schadt
Jul 26, 2012·Genome Research·Filipe J RibeiroDavid B Jaffe
Sep 17, 2013·Genome Biology·Sergey KorenAdam M Phillippy
Jun 22, 2014·BMC Bioinformatics·Marten Boetzer, Walter Pirovano

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.