NDLI: Probability Model for Boundaries of Short-Read Sequencing

Content Provider	IEEE Xplore Digital Library
Author	Schatz, F. Wienbrandt, L. Schimmler, M.
Copyright Year	2012
Abstract	The need for sequencing DNA has been growing tremendously over the past few years. Current next-generation sequencing techniques produce huge amounts of data but time and money remain limiting factors for researchers. Given a DNA sample, it is essential to produce a sufficient number of reads to create or recreate a digital representation of the DNA while minimizing the needed resources. This work proposes a theoretical model that yields a set of formulas to calculate amongst others the expected distribution of contig length and estimated N50 value for a low-coverage, short-read sequencing experiment. The formulas can be used as an extension to the well known Lander-Waterman model to model assembly projects. The only input parameters these formulas are based on are the DNA sequence length, the number of reads and the read length. These formulas can provide boundaries (e.g. N50) that can be calculated before a sequencing process in order to reduce or adjust the needed resources for resequencing or de novo assembly and to get enough, but not too much, information or estimate the feasibility of a sequencing project.
Starting Page	223
Ending Page	228
File Size	293366
Page Count	6
File Format	PDF
ISBN	9781467319119
DOI	10.1109/ICACC.2012.51
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-08-09
Publisher Place	India
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Statistical genetics Multiple sequence alignment Genomics Humans Estimation Coverage Alignment Next-generation sequencing DNA Data models Bioinformatics Sequencing Assembly
Content Type	Text
Resource Type	Article

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