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Mappability and read length.

Wentian Li1, Jan Freudenberg1

  • 1The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System Manhasset, NY, USA.

Frontiers in Genetics
|November 27, 2014
PubMed
Summary
This summary is machine-generated.

Human genome sequencing faces challenges with repetitive DNA sequences. Longer reads improve mapping but encounter diminishing returns due to the nature of repeat distributions.

Keywords:
copy number variationsmappabilitynext-generation sequencingpower-law distributionrepeats

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Repetitive DNA sequences are prevalent in the human genome, often following power-law distributions for size and copy number.
  • The fragmentation of genomes for sequencing can lead to unmappable reads from these repetitive regions.

Purpose of the Study:

  • To analyze the impact of read length on the mappability of repetitive sequences in the human genome.
  • To understand the relationship between sequencing read length and the proportion of uniquely aligned reads.

Main Methods:

  • Analysis of sequence read mapping statistics based on varying read lengths.
  • Characterization of repeat distributions using power-law functions.

Main Results:

  • A significant portion of human genome reads can be unmappable due to repetitive elements, particularly with shorter read lengths (e.g., 1 kb reads).
  • Increasing read length enhances mappability, but the power-law distribution of repeats results in diminishing returns.

Conclusions:

  • Repetitive DNA poses a fundamental challenge in achieving complete genome sequence mappability.
  • While longer reads are beneficial, the inherent properties of genomic repeats limit the extent to which mappability can be improved.