ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.
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ABSTRACT:
SUBMITTER: Maccallum I
PROVIDER: S-EPMC2784318 | biostudies-literature | 2009
REPOSITORIES: biostudies-literature
Publications
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.
Maccallum Iain I Przybylski Dariusz D Gnerre Sante S Burton Joshua J Shlyakhter Ilya I Gnirke Andreas A Malek Joel J McKernan Kevin K Ranade Swati S Shea Terrance P TP Williams Louise L Young Sarah S Nusbaum Chad C Jaffe David B DB
Genome biology 20091001 10
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). ...[more]
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