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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~100-base) sequence reads at very low cost. Whereas suchExpand
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Evolution of genes and genomes on the Drosophila phylogeny
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genomeExpand
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ALLPATHS: de novo assembly of whole-genome shotgun microreads.
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial,Expand
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Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe theExpand
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The genomic substrate for adaptive radiation in African cichlid fish
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, weExpand
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequencesExpand
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Comprehensive variation discovery in single human genomes
Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencingExpand
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The African coelacanth genome provides insights into tetrapod evolution.
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looksExpand
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ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of variedExpand
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Paired-end sequencing of Fosmid libraries by Illumina.
Eliminating the bacterial cloning step has been a major factor in the vastly improved efficiency of massively parallel sequencing approaches. However, this also has made it a technical challenge toExpand
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