Sequence assembly

Karsten Scheibye-Alsing; S. Hoffmann; Annett Maria Frankel; Peter Jensen; P.F. Stadler; Yuan Mang; Niels Tommerup; M.J. Gilchrist; Ann-Britt Nygaard Hillig; Susanna Cirera Salicio; Claus Bøttcher Jørgensen; Merete Fredholm; Jan Gorodkin

doi:10.1016/j.compbiolchem.2008.11.003

Sequence assembly

Karsten Scheibye-Alsing, S. Hoffmann, Annett Maria Frankel, Peter Jensen, P.F. Stadler, Yuan Mang, Niels Tommerup, M.J. Gilchrist, Ann-Britt Nygaard Hillig, Susanna Cirera Salicio, Claus Bøttcher Jørgensen, Merete Fredholm, Jan Gorodkin

Department of Cellular and Molecular Medicine

36 Citations (Scopus)

Abstract

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.

Original language	English
Journal	Computational Biology and Chemistry
Volume	33
Issue number	2
Pages (from-to)	121-136
Number of pages	16
ISSN	1476-9271
DOIs	https://doi.org/10.1016/j.compbiolchem.2008.11.003
Publication status	Published - 2009

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title = "Sequence assembly",

abstract = "Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.",

author = "Karsten Scheibye-Alsing and S. Hoffmann and Frankel, {Annett Maria} and Peter Jensen and P.F. Stadler and Yuan Mang and Niels Tommerup and M.J. Gilchrist and Hillig, {Ann-Britt Nygaard} and {Cirera Salicio}, Susanna and J{\o}rgensen, {Claus B{\o}ttcher} and Merete Fredholm and Jan Gorodkin",

year = "2009",

doi = "10.1016/j.compbiolchem.2008.11.003",

language = "English",

volume = "33",

pages = "121--136",

journal = "Computational Biology and Chemistry",

issn = "1476-9271",

publisher = "Elsevier",

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TY - JOUR

T1 - Sequence assembly

AU - Scheibye-Alsing, Karsten

AU - Hoffmann, S.

AU - Frankel, Annett Maria

AU - Jensen, Peter

AU - Stadler, P.F.

AU - Mang, Yuan

AU - Tommerup, Niels

AU - Gilchrist, M.J.

AU - Hillig, Ann-Britt Nygaard

AU - Cirera Salicio, Susanna

AU - Jørgensen, Claus Bøttcher

AU - Fredholm, Merete

AU - Gorodkin, Jan

PY - 2009

Y1 - 2009

N2 - Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.

AB - Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.

U2 - 10.1016/j.compbiolchem.2008.11.003

DO - 10.1016/j.compbiolchem.2008.11.003

M3 - Review

C2 - 19152793

SN - 1476-9271

VL - 33

SP - 121

EP - 136

JO - Computational Biology and Chemistry

JF - Computational Biology and Chemistry

IS - 2

ER -

Sequence assembly

Abstract

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