Assisted assembly: how to improve a de novo genome assembly by using related species.
We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.
Gnerre
Sante
S
Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA. sante@broad.mit.edu
Lander
Eric S
ES
Lindblad-Toh
Kerstin
K
Jaffe
David B
DB
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D006801:Humans; D008322:Mammals / Q000235:genetics; D010961:Plasmodium / Q000235:genetics