Whole-genome sequence assembly for mammalian genomes: Arachne 2.
By David B. Jaffe, Jonathan Butler, S. Gnerre, E. Mauceli, Kerstin Lindblad-Toh, Jill P. Mesirov, M. Zody, Eric S. Lander. Genome Research, 2003
344 citations recorded by the source corpus.
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).
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/42739f1f1f7dea6cd7552a5f15b5d32ac9cfee0a
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In Molecular Biology
- Steven L. Salzberg
- Mihai Pop
- Sergey Koren
- Pavel A. Pevzner
- Mark J. P. Chaisson
- Eric S. Lander
- Brian Walenz
- Erez Lieberman Aiden
In Plant Science
- Pavel A. Pevzner
- Mark J. P. Chaisson
- Eric S. Lander
- Natalia N. Ivanova
- Erez Lieberman Aiden
- Brian Walenz
- Sergey Koren
- Mihai Pop
Citations in the corpus
- Quality scores and SNP detection in sequencing-by-synthesis systems. (2008, positive): “We used the QueryLookupTable aligner developed for ARACHNE (Jaffe et al. 2003).”
- The fragment assembly string graph (2005, background): “…capable of wholegenome assembly that all perform comparably by employing variations on the basic paradigm of first finding and assembling unique stretches of DNA with high reliability (Myers et al., 2000; Aparicio et al., 2002; Mullikin and Ning, 2003; Jaffe et al., 2003; Huang et al., 2003).”