NDLI: Base calling for high-throughput short-read sequencing: dynamic programming solutions

Content Provider	Springer Nature : BioMed Central
Author	Das, Shreepriya Vikalo, Haris
Abstract	Background Next-generation DNA sequencing platforms are capable of generating millions of reads in a matter of days at rapidly reducing costs. Despite its proliferation and technological improvements, the performance of next-generation sequencing remains adversely affected by the imperfections in the underlying biochemical and signal acquisition procedures. To this end, various techniques, including statistical methods, are used to improve read lengths and accuracy of these systems. Development of high performing base calling algorithms that are computationally efficient and scalable is an ongoing challenge. Results We develop model-based statistical methods for fast and accurate base calling in Illumina’s next-generation sequencing platforms. In particular, we propose a computationally tractable parametric model which enables dynamic programming formulation of the base calling problem. Forward-backward and soft-output Viterbi algorithms are developed, and their performance and complexity are investigated and compared with the existing state-of-the-art base calling methods for this platform. A C code implementation of our algorithm named Softy can be downloaded from https://sourceforge.net/projects/dynamicprog . Conclusion We demonstrate high accuracy and speed of the proposed methods on reads obtained using Illumina’s Genome Analyzer II and HiSeq2000. In addition to performing reliable and fast base calling, the developed algorithms enable incorporation of prior knowledge which can be utilized for parameter estimation and is potentially beneficial in various downstream applications.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-129.pdf
Ending Page	10
Page Count	10
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/1471-2105-14-129
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	14
Language	English
Publisher	BioMed Central
Publisher Date	2013-04-15
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Base Calling Posteriori Probability Viterbi Algorithm Dynamic Programming Formulation Parameter Estimation Step Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Base calling for high-throughput short-read sequencing: dynamic programming solutions