An Integrated Approach to Comparative Assembly

Desmond Chambers

An Integrated Approach to Comparative Assembly

Desmond Chambers

Computer Science

Research output: Chapter in Book or Conference Publication/Proceeding › Conference Publication › peer-review

Abstract

We describe a novel approach to comparative assembly that directly integrates anchoring alignments into the contig assembly process, enabling the extension of contig construction through the boundaries of repeat nodes in a compressed de Bruijn graph. Our method exploits anchoring alignments, paired-read constraints and read threading as path selection heuristics while an assembly graph is transversed during contig construction. Tests and benchmarks against preeminent implementations of both comparative and de novo assembly models demonstrate that the approach can significantly increase the contiguity of an assembly without inducing a large number of misjoins and structural errors.

Original language	English (Ireland)
Title of host publication	PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2
Publisher	COPICENTRO GRANADA S L
Number of pages	11
Publication status	Published - 1 Jan 2014

Authors (Note for portal: view the doc link for the full list of authors)

Authors
Healy, J;Chambers, D

Cite this

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title = "An Integrated Approach to Comparative Assembly",

abstract = "We describe a novel approach to comparative assembly that directly integrates anchoring alignments into the contig assembly process, enabling the extension of contig construction through the boundaries of repeat nodes in a compressed de Bruijn graph. Our method exploits anchoring alignments, paired-read constraints and read threading as path selection heuristics while an assembly graph is transversed during contig construction. Tests and benchmarks against preeminent implementations of both comparative and de novo assembly models demonstrate that the approach can significantly increase the contiguity of an assembly without inducing a large number of misjoins and structural errors.",

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AB - We describe a novel approach to comparative assembly that directly integrates anchoring alignments into the contig assembly process, enabling the extension of contig construction through the boundaries of repeat nodes in a compressed de Bruijn graph. Our method exploits anchoring alignments, paired-read constraints and read threading as path selection heuristics while an assembly graph is transversed during contig construction. Tests and benchmarks against preeminent implementations of both comparative and de novo assembly models demonstrate that the approach can significantly increase the contiguity of an assembly without inducing a large number of misjoins and structural errors.

M3 - Conference Publication

BT - PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2

PB - COPICENTRO GRANADA S L

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An Integrated Approach to Comparative Assembly

Abstract

Authors (Note for portal: view the doc link for the full list of authors)

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