Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

• DOI: 10.1101/gr.828403
• Publication Date: 2003-01-15T18:22:25Z
• Authors: David B. Jaffe; Jonathan Butler; Sante Gnerre; Evan Mauceli; Kerstin Lindblad-Toh; Jill P. Mesirov; Michael C. Zody; Eric S. Lander
• Keywords: Sequence assembly; Hybrid genome assembly; Sequence (biology)

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 program, allowing mammalian-size genomes, and also improving smaller Three principal changes were simultaneously made applied mouse genome, during a six-month period development: (1) Supercontigs (scaffolds) iteratively broken rejoined using several criteria, yielding 64-fold increase in length (N50), apparent elimination all global misjoins; (2) gaps between contigs supercontigs filled (partially or completely) by insertion reads, as suggested pairing within supercontig, increasing N50 contig 50%; (3) memory usage was reduced fourfold. The outcome this its analysis are (Mouse Genome Sequencing Consortium 2002).