Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.
Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assembled data frequently are highly fragmented with many gaps. We present a practical approach that uses Illumina sequences to improve draft genome assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. The continuity of a draft genome can thus be substantially improved, often without the need to generate new data.
Tsai
Isheng J
IJ
Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. jit@sanger.ac.uk
Otto
Thomas D
TD
Berriman
Matthew
M
D000465:Algorithms; D001483:Base Sequence; D020451:Contig Mapping; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
Genome Res. 2001 Oct;11(10):1725-9
11591649
Genome Res. 1998 Nov;8(11):1097-108
9847074
PCR Methods Appl. 1991 Nov;1(2):124-8
1842929
Nucleic Acids Res. 1995 Dec 25;23(24):4992-9
8559656
Genome Res. 2001 Apr;11(4):614-25
11282977
Genome Res. 2008 May;18(5):821-9
18349386
Genome Biol. 2009;10(10):R103
19796385
Nature. 2008 Nov 6;456(7218):53-9
18987734
Genome Res. 2002 Jan;12(1):177-89
11779843
Bioinformatics. 2009 Aug 15;25(16):2078-9
19505943
Genome Res. 2009 Jun;19(6):1117-23
19251739
Genome Res. 2003 Jan;13(1):81-90
12529309
Genome Res. 2009 Feb;19(2):294-305
19015323
Bioinformatics. 2009 Aug 1;25(15):1968-9
19497936
Genome Biol. 2009;10(3):R32
19327155
Genome Res. 2010 Feb;20(2):265-72
20019144
Science. 2009 Oct 9;326(5950):236-7
19815760
Genome Biol. 2009;10(9):R94
19747388