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The greedy path-merging algorithm for contig scaffolding

Authors:

Daniel H. Huson,

Knut Reinert,

Eugene W. MyersAuthors Info & Claims

Journal of the ACM (JACM), Volume 49, Issue 5

Pages 603 - 615

https://doi.org/10.1145/585265.585267

Published: 01 September 2002 Publication History

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Abstract

Given a collection of contigs and mate-pairs. The Contig Scaffolding Problem is to order and orientate the given contigs in a manner that is consistent with as many mate-pairs as possible. This paper describes an efficient heuristic called the greedy-path merging algorithm for solving this problem. The method was originally developed as a key component of the compartmentalized assembly strategy developed at Celera Genomics. This interim approach was used at an early stage of the sequencing of the human genome to produce a preliminary assembly based on preliminary whole genome shotgun data produced at Celera and preliminary human contigs produced by the Human Genome Project.

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Index Terms

The greedy path-merging algorithm for contig scaffolding
1. Applied computing
  1. Life and medical sciences
2. Theory of computation
  1. Randomness, geometry and discrete structures

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Information

Published In

Journal of the ACM Volume 49, Issue 5

September 2002

137 pages

ISSN:0004-5411

EISSN:1557-735X

DOI:10.1145/585265

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 01 September 2002

Published in JACM Volume 49, Issue 5

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Epain VAndonov R(2024)Global exact optimisations for chloroplast structural haplotype scaffoldingAlgorithms for Molecular Biology10.1186/s13015-023-00243-119:1Online publication date: 6-Feb-2024
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Bhowmik ORahman TKalyanaraman A(2024)Maptcha: an efficient parallel workflow for hybrid genome scaffoldingBMC Bioinformatics10.1186/s12859-024-05878-425:1Online publication date: 8-Aug-2024
https://doi.org/10.1186/s12859-024-05878-4
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Zhao JZhang SWu SZhang WSu X(2023)Current Progress of Bioinformatics for Human HealthMethodologies of Multi-Omics Data Integration and Data Mining10.1007/978-981-19-8210-1_8(145-162)Online publication date: 16-Jan-2023
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