Whole-genome sequence assembly for mammalian genomes: Arachne 2.
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).
Jaffe
David B
DB
Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA. jaffe@genome.wi.mit.edu
Butler
Jonathan
J
Gnerre
Sante
S
Mauceli
Evan
E
Lindblad-Toh
Kerstin
K
Mesirov
Jill P
JP
Zody
Michael C
MC
Lander
Eric S
ES
D000818:Animals; D019295:Computational Biology / Q000379:methods; D020451:Contig Mapping / Q000379:methods; D016678:Genome; D006801:Humans; D051379:Mice; D012984:Software