%0 Journal Article %1 Jaffe:2003aa %A Jaffe, David B %A Butler, Jonathan %A Gnerre, Sante %A Mauceli, Evan %A Lindblad-Toh, Kerstin %A Mesirov, Jill P %A Zody, Michael C %A Lander, Eric S %D 2003 %J Genome Res %K Animals, Biology, Computational Contig Genome, Humans Mapping, Mice, Software, %N 1 %P 91--6 %R 10.1101/gr.828403 %T Whole-genome sequence assembly for mammalian genomes: Arachne 2 %V 13 %X 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).

@article{Jaffe:2003aa, 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).}, added-at = {2007-09-17T20:19:41.000+0200}, affiliation = {Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA. jaffe@genome.wi.mit.edu}, 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}, biburl = {https://www.bibsonomy.org/bibtex/2c9787f374c7933c38f7ab5214fb93862/dzerbino}, doi = {10.1101/gr.828403}, interhash = {a56b449830923e2399817ee015844488}, intrahash = {c9787f374c7933c38f7ab5214fb93862}, issue = {1}, journal = {Genome Res}, keywords = {Animals, Biology, Computational Contig Genome, Humans Mapping, Mice, Software,}, language = {English}, local-url = {file://localhost/Users/danielzerbino/Documents/Papers/2003/Jaffe/Genome%20Res%202003%20Jaffe.pdf}, month = Jan, number = 1, pages = {91--6}, pmid = {12529310}, timestamp = {2007-09-17T20:19:42.000+0200}, title = {Whole-genome sequence assembly for mammalian genomes: Arachne 2}, uri = {papers://055852FE-1648-42FE-91D0-8CA474D2B905/Paper/p12}, volume = 13, year = 2003 }