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    Genome Res. 2003 Jan;13(1):91-6.

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

    Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES.

    Source

    Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA. jaffe@genome.wi.mit.edu

    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).

    PMID:
    12529310
    [PubMed - indexed for MEDLINE]
    PMCID: PMC430950
    Free PMC Article

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