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).
Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA. iainm@broadinstitute.org
Iain
I
Maccallum
Dariusz
D
Przybylski
Sante
S
Gnerre
Joshua
J
Burton
Ilya
I
Shlyakhter
Andreas
A
Gnirke
Joel
J
Malek
Kevin
K
McKernan
Swati
S
Ranade
Terrance P
TP
Shea
Louise
L
Williams
Sarah
S
Young
Chad
C
Nusbaum
David B
DB
Jaffe
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