OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Bioinformatics
Shreepriya Das, Haris Vikalo

Abstract

Next-generation DNA sequencing platforms are becoming increasingly cost-effective and capable of providing enormous number of reads in a relatively short time. However, their accuracy and read lengths are still lagging behind those of conventional Sanger sequencing method. Performance of next-generation sequencing platforms is fundamentally limited by various imperfections in the sequencing-by-synthesis and signal acquisition processes. This drives the search for accurate, scalable and computationally tractable base calling algorithms capable of accounting for such imperfections. Relying on a statistical model of the sequencing-by-synthesis process and signal acquisition procedure, we develop a computationally efficient base calling method for Illumina's sequencing technology (specifically, Genome Analyzer II platform). Parameters of the model are estimated via a fast unsupervised online learning scheme, which uses the generalized expectation-maximization algorithm and requires only 3 s of running time per tile (on an Intel i7 machine @3.07GHz, single core)-a three orders of magnitude speed-up over existing parametric model-based methods. To minimize the latency between the end of the sequencing run and the generation of the ba...Continue Reading

References

Mar 1, 2008·BMC Bioinformatics·Andrew D SmithMichael Q Zhang
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Jun 26, 2008·Annual Review of Genomics and Human Genetics·Elaine R Mardis
Jul 8, 2008·Nature Methods·Yaniv ErlichGregory J Hannon
Oct 15, 2008·BMC Bioinformatics·Jacques RougemontFelix Naef
Nov 7, 2008·Nature·David R BentleyAnthony J Smith

❮ Previous
Next ❯

Citations

Apr 17, 2013·BMC Bioinformatics·Shreepriya Das, Haris Vikalo
Oct 9, 2015·Thrombosis and Haemostasis·Marisa L R CunhaSaskia Middeldorp
May 31, 2015·Bioinformatics·Greg MalysaTsachy Weissman
Oct 8, 2015·Briefings in Bioinformatics·Ashley CachoXinping Cui
Jul 9, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Eliza O'ReillyHaris Vikalo
Jun 30, 2016·Bioinformatics·Daniel L GreenfieldAlban Rrustemi
Mar 29, 2018·BMC Genomics·Abolfazl HashemiHaris Vikalo
Sep 18, 2020·Journal of Bioinformatics and Computational Biology·Albert NoIdoia Ochoa
Apr 18, 2015·BMC Genomics·Shreepriya Das, Haris Vikalo
Sep 13, 2020·Journal of Agricultural and Food Chemistry·Doreen TeskeMarkus Fischer

❮ 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.