ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Genome biology, 2009•Springer
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).
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).
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).
Springer
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