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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
- S. Gnerre, Iain Maccallum, D. Jaffe
- BiologyProceedings of the National Academy of Sciences
- 27 December 2010
The development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform, have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome.
Evolution of genes and genomes on the Drosophila phylogeny
These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
ALLPATHS: de novo assembly of whole-genome shotgun microreads.
A general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads is described.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
The high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
The Assemblathon 1 competition is described, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies, and it is established that it is possible to assemble the genome to a high level of coverage and accuracy.
The genomic substrate for adaptive radiation in African cichlid fish
It is concluded that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
The African coelacanth genome provides insights into tetrapod evolution.
Through a phylogenomic analysis, it is concluded that the lungfish, and not the coelacanth, is the closest living relative of tetrapods.
Comprehensive variation discovery in single human genomes
It is shown that the combination of new methods and improved data increases sensitivity by several fold, with the greatest impact in challenging regions of the human genome.
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds.
Finished bacterial genomes from shotgun sequence data.
By applying a new laboratory design and new assembly algorithm to 16 samples, it is demonstrated that assemblies exceeding finished quality can be obtained from whole-genome shotgun data and automated computation.