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Updated: Jun 19, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Iain Maccallum1, Dariusz Przybylski, Sante Gnerre
1Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA. iainm@broadinstitute.org
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).
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