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
Descripción
Sumario: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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