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

Iain MacCallum; Dariusz Przybylski; Sante Gnerre; Joshua Burton; Ilya Shlyakhter; Andreas Gnirke; Joel Malek; Kevin McKernan; Swati Ranade; Terrance P Shea; Louise Williams; Sarah Young; Chad Nusbaum; David B Jaffe

doi:10.1186/gb-2009-10-10-r103

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

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

Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, …

GenomeBiology.com, Vol.10(10), pp.R103-R103

10/01/2009

DOI: https://doi.org/10.1186/gb-2009-10-10-r103

PMCID: PMC2784318

PMID: 19796385

Abstract

Reference Sequence

Additional Data File

Base Accuracy

Bacterial Assembly

Single Base Mismatch

Allpaths2, a method for accurately assembling small genomes with high continuity using 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 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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Title: ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Creators: Iain MacCallum - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Dariusz Przybylski - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Sante Gnerre - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Joshua Burton - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Ilya Shlyakhter - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Andreas Gnirke - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Joel Malek - Life Technologies, Cummings Center, Beverly, MA 01915, USA
Kevin McKernan - Life Technologies, Cummings Center, Beverly, MA 01915, USA
Swati Ranade - Life Technologies, Cummings Center, Beverly, MA 01915, USA
Terrance P Shea - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Louise Williams - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Sarah Young - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Chad Nusbaum - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
David B Jaffe - Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
Publication Details: GenomeBiology.com, Vol.10(10), pp.R103-R103
Publisher: BioMed Central
Identifiers: 9924012910501921
Academic Unit: Department of Biology
Language: English
Resource Type: Journal article

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

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