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Optimal assembly for high throughput shotgun sequencing

BMC Bioinformatics

Nov 6, 2013

Guy BreslerDavid N Tse

Abstract

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Buil...read more

Mentioned in this Paper

Genome
Nucleic Acid Hybridization Procedure
Analog
Sequencing
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Contig Mapping
Shotgun Sequencing
Crossbreeding
DNA Sequence
11
136
Paper Details
References
  • References17
  • Citations4
12
  • References17
  • Citations4
1

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Optimal assembly for high throughput shotgun sequencing

BMC Bioinformatics

Nov 6, 2013

Guy BreslerDavid N Tse

PMID: 23902516

DOI: 10.1186/1471-2105-14-s5-s18

Abstract

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Buil...read more

Mentioned in this Paper

Genome
Nucleic Acid Hybridization Procedure
Analog
Sequencing
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Contig Mapping
Shotgun Sequencing
Crossbreeding
DNA Sequence
11
136

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.

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Estimating the repeat structure and length of DNA sequences using L-tuples

Genome ResearchAugust 7, 2003
Xiaoman Li, M S Waterman
Paper Details
References
  • References17
  • Citations4
12
  • References17
  • Citations4
1

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