ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Academic Article uri icon

Overview

abstract

  • 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).

publication date

  • October 1, 2009

Research

keywords

  • Bacteria
  • Fungi
  • Genome
  • Genomics
  • Software

Identity

PubMed Central ID

  • PMC2784318

Scopus Document Identifier

  • 75349109607

Digital Object Identifier (DOI)

  • 10.1073/pnas.81.21.6812

PubMed ID

  • 19796385

Additional Document Info

volume

  • 10

issue

  • 10