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 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).
Maccallum
Iain
I
Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA. iainm@broadinstitute.org
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
D001419:Bacteria / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics; D005658:Fungi / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software