The greedy path-merging algorithm for contig scaffolding-Reference-Cited by-同舟云学术

The greedy path-merging algorithm for contig scaffolding

Published:2002-09 Issue:5 Volume:49 Page:603-615
ISSN:0004-5411
Container-title:Journal of the ACM
language:en
Short-container-title:J. ACM

Author:

Huson Daniel H.¹,Reinert Knut²,Myers Eugene W.³

Affiliation:

1. Tübingen University, Tübingen, Germany

2. Free University Berlin, Berlin, Germany

3. University of California Berkeley, Berkeley, CA

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.

Publisher

Association for Computing Machinery (ACM)

Subject

Artificial Intelligence,Hardware and Architecture,Information Systems,Control and Systems Engineering,Software

Link

https://dl.acm.org/doi/pdf/10.1145/585265.585267

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