Whole-genome sequence assembly for mammalian genomes: Arachne 2.

@article{citeulike:622628, 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).}, address = {Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA. jaffe@genome.wi.mit.edu}, author = {Jaffe, D. B. and Butler, J. and Gnerre, S. and Mauceli, E. and Lindblad-Toh, K. and Mesirov, J. P. and Zody, M. C. and Lander, E. S. }, citeulike-article-id = {622628}, doi = {10.1101/gr.828403}, issn = {1088-9051}, journal = {Genome Res}, keywords = {algorithm, assembly}, month = {January}, number = {1}, pages = {91--96}, posted-at = {2007-12-03 12:32:59}, priority = {2}, title = {Whole-genome sequence assembly for mammalian genomes: Arachne 2.}, url = {http://dx.doi.org/10.1101/gr.828403}, volume = {13}, year = {2003} }

TY - JOUR ID - citeulike:622628 L3 - citeulike-article-id:622628 TI - Whole-genome sequence assembly for mammalian genomes: Arachne 2. JF - Genome Res VL - 13 IS - 1 SP - 91 EP - 96 AD - Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA. jaffe@genome.wi.mit.edu SN - 1088-9051 N2 - 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). KW - algorithm KW - assembly AU - Jaffe, DB AU - Butler, J AU - Gnerre, S AU - Mauceli, E AU - Lindblad-Toh, K AU - Mesirov, JP AU - Zody, MC AU - Lander, ES PY - 2003/01// UR - http://dx.doi.org/10.1101/gr.828403 ER -