ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and...

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Detalles Bibliográficos
Autores principales: MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Shlyakhter, Ilya, Gnirke, Andreas, Malek, Joel, McKernan, Kevin, Ranade, Swati, Shea, Terrance P, Williams, Louise, Young, Sarah, Nusbaum, Chad, Jaffe, David B
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784318/
https://www.ncbi.nlm.nih.gov/pubmed/19796385
http://dx.doi.org/10.1186/gb-2009-10-10-r103
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author MacCallum, Iain
Przybylski, Dariusz
Gnerre, Sante
Burton, Joshua
Shlyakhter, Ilya
Gnirke, Andreas
Malek, Joel
McKernan, Kevin
Ranade, Swati
Shea, Terrance P
Williams, Louise
Young, Sarah
Nusbaum, Chad
Jaffe, David B
author_facet MacCallum, Iain
Przybylski, Dariusz
Gnerre, Sante
Burton, Joshua
Shlyakhter, Ilya
Gnirke, Andreas
Malek, Joel
McKernan, Kevin
Ranade, Swati
Shea, Terrance P
Williams, Louise
Young, Sarah
Nusbaum, Chad
Jaffe, David B
author_sort MacCallum, Iain
collection PubMed
description We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR).
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spelling pubmed-27843182009-11-27 ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads MacCallum, Iain Przybylski, Dariusz Gnerre, Sante Burton, Joshua Shlyakhter, Ilya Gnirke, Andreas Malek, Joel McKernan, Kevin Ranade, Swati Shea, Terrance P Williams, Louise Young, Sarah Nusbaum, Chad Jaffe, David B Genome Biol Method We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR). BioMed Central 2009 2009-10-01 /pmc/articles/PMC2784318/ /pubmed/19796385 http://dx.doi.org/10.1186/gb-2009-10-10-r103 Text en Copyright ©2009 MacCallum et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
MacCallum, Iain
Przybylski, Dariusz
Gnerre, Sante
Burton, Joshua
Shlyakhter, Ilya
Gnirke, Andreas
Malek, Joel
McKernan, Kevin
Ranade, Swati
Shea, Terrance P
Williams, Louise
Young, Sarah
Nusbaum, Chad
Jaffe, David B
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
title ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
title_full ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
title_fullStr ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
title_full_unstemmed ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
title_short ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
title_sort allpaths 2: small genomes assembled accurately and with high continuity from short paired reads
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784318/
https://www.ncbi.nlm.nih.gov/pubmed/19796385
http://dx.doi.org/10.1186/gb-2009-10-10-r103
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