REAL: an efficient REad ALigner for next generation sequencing reads

Kimon Frousios; Costas S. Iliopoulos; Laurent Mouchard; Solon P. Pissis; German Tischler

doi:10.1145/1854776.1854801

REAL: an efficient REad ALigner for next generation sequencing reads

Kimon Frousios, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis, German Tischler

Informatics

Research output: Chapter in Book/Report/Conference proceeding › Conference paper

25 Citations (Scopus)

Abstract

Motivation: The constant advances in sequencing technology are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data in the form of short reads need to be mapped back to reference sequences, a few gigabases long. A first generation of short read alignment software successfully employed hash tables, and the current second generation uses Burrows-Wheeler Transform, further improving mapping speed. However, there is still demand for faster and more accurate mapping.

Results: In this paper, we present REad ALigner, an efficient, accurate and consistent tool for aligning short reads obtained from next generation sequencing. It is based on a new, simple, yet efficient mapping algorithm that can match and outperform current BWT-based software.

Original language	English
Title of host publication	BCB '10 Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Publisher	ACM
Pages	154-159
Number of pages	6
ISBN (Print)	978-1-4503-0438-2
DOIs	https://doi.org/10.1145/1854776.1854801
Publication status	Published - 2010
Event	BCB' 10 ACM International Conference on Bioinformatics and Computational Biology - Niagara Falls, NY, United States Duration: 2 Aug 2010 → 4 Aug 2010

Conference

Conference	BCB' 10 ACM International Conference on Bioinformatics and Computational Biology
Country/Territory	United States
City	Niagara Falls, NY
Period	2/08/2010 → 4/08/2010

Keywords

mapping, next generation sequencing, pattern matching, reads, string algorithms

Access to Document

10.1145/1854776.1854801

Cite this

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title = "REAL: an efficient REad ALigner for next generation sequencing reads",

abstract = "Motivation: The constant advances in sequencing technology are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data in the form of short reads need to be mapped back to reference sequences, a few gigabases long. A first generation of short read alignment software successfully employed hash tables, and the current second generation uses Burrows-Wheeler Transform, further improving mapping speed. However, there is still demand for faster and more accurate mapping.Results: In this paper, we present REad ALigner, an efficient, accurate and consistent tool for aligning short reads obtained from next generation sequencing. It is based on a new, simple, yet efficient mapping algorithm that can match and outperform current BWT-based software.",

keywords = "mapping, next generation sequencing, pattern matching, reads, string algorithms",

author = "Kimon Frousios and Iliopoulos, {Costas S.} and Laurent Mouchard and Pissis, {Solon P.} and German Tischler",

year = "2010",

doi = "10.1145/1854776.1854801",

language = "English",

isbn = "978-1-4503-0438-2",

pages = "154--159",

booktitle = "BCB '10 Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology",

publisher = "ACM",

note = "BCB' 10 ACM International Conference on Bioinformatics and Computational Biology ; Conference date: 02-08-2010 Through 04-08-2010",

}

Frousios, K , Iliopoulos, CS , Mouchard, L , Pissis, SP & Tischler, G 2010, REAL: an efficient REad ALigner for next generation sequencing reads. in BCB '10 Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology. ACM, pp. 154-159, BCB' 10 ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY, United States, 2/08/2010. https://doi.org/10.1145/1854776.1854801

TY - CHAP

T1 - REAL: an efficient REad ALigner for next generation sequencing reads

AU - Frousios, Kimon

AU - Iliopoulos, Costas S.

AU - Mouchard, Laurent

AU - Pissis, Solon P.

AU - Tischler, German

PY - 2010

Y1 - 2010

N2 - Motivation: The constant advances in sequencing technology are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data in the form of short reads need to be mapped back to reference sequences, a few gigabases long. A first generation of short read alignment software successfully employed hash tables, and the current second generation uses Burrows-Wheeler Transform, further improving mapping speed. However, there is still demand for faster and more accurate mapping.Results: In this paper, we present REad ALigner, an efficient, accurate and consistent tool for aligning short reads obtained from next generation sequencing. It is based on a new, simple, yet efficient mapping algorithm that can match and outperform current BWT-based software.

AB - Motivation: The constant advances in sequencing technology are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data in the form of short reads need to be mapped back to reference sequences, a few gigabases long. A first generation of short read alignment software successfully employed hash tables, and the current second generation uses Burrows-Wheeler Transform, further improving mapping speed. However, there is still demand for faster and more accurate mapping.Results: In this paper, we present REad ALigner, an efficient, accurate and consistent tool for aligning short reads obtained from next generation sequencing. It is based on a new, simple, yet efficient mapping algorithm that can match and outperform current BWT-based software.

KW - mapping, next generation sequencing, pattern matching, reads, string algorithms

U2 - 10.1145/1854776.1854801

DO - 10.1145/1854776.1854801

M3 - Conference paper

SN - 978-1-4503-0438-2

SP - 154

EP - 159

BT - BCB '10 Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology

PB - ACM

T2 - BCB' 10 ACM International Conference on Bioinformatics and Computational Biology

Y2 - 2 August 2010 through 4 August 2010

ER -

REAL: an efficient REad ALigner for next generation sequencing reads

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Keywords

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