Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
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).
Footnotes
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↵2 Corresponding author.
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E-MAIL jaffe{at}genome.wi.mit.edu; FAX (617) 258-9108.
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.828403.
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- Received September 19, 2002.
- Accepted October 30, 2002.
- Cold Spring Harbor Laboratory Press
