Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

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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).

Ingår i:Genome Research: Cold Spring Harbor Laboratory13:1, s. 91-961088-90511549-5469

Av författaren/redakt...: Jaffe, David B.; Butler, Jonathan; Gnerre, Sante; Mauceli, Evan; Lindblad-Toh, Ke ...; Mesirov, Jill P.; visa fler...; Zody, Michael C.; Lander, Eric S.; visa färre...

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