@article{Jaffe01012003,
author = {Jaffe, David B. and Butler, Jonathan and Gnerre, Sante and Mauceli, Evan and Lindblad-Toh, Kerstin and Mesirov, Jill P. and Zody, Michael C. and Lander, Eric S.}, 
title = {Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2},
volume = {13}, 
number = {1}, 
pages = {91-96}, 
year = {2003}, 
doi = {10.1101/gr.828403}, 
abstract ={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).}, 
URL = {http://genome.cshlp.org/content/13/1/91.abstract}, 
eprint = {http://genome.cshlp.org/content/13/1/91.full.pdf+html}, 
journal = {Genome Research} 
}