RT Journal
A1 Jaffe, David B.
A1 Butler, Jonathan
A1 Gnerre, Sante
A1 Mauceli, Evan
A1 Lindblad-Toh, Kerstin
A1 Mesirov, Jill P.
A1 Zody, Michael C.
A1 Lander, Eric S.
T1 Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
JF Genome Research 
JO Genome Research 
YR 2003 
FD January 01 
VO 13 
IS 1 
SP 91 
OP 96 
DO 10.1101/gr.828403 
UL http://genome.cshlp.org/content/13/1/91.abstract 
AB 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).