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ABySS: a parallel assembler for short read sequence data.
- J. Simpson, K. Wong, S. Jackman, J. Schein, S. Jones, I. Birol
- Biology, Medicine
- Genome research
- 1 June 2009
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the… Expand
Efficient de novo assembly of large genomes using compressed data structures.
De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome sequence of individuals in a… Expand
A complete bacterial genome assembled de novo using only nanopore sequencing data
We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then… Expand
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 the… Expand
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
We provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). Expand
Nanopore sequencing and assembly of a human genome with ultra-long reads
Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However… Expand
Detecting DNA cytosine methylation using nanopore sequencing
- J. Simpson, R. Workman, P. Zuzarte, M. David, L. Dursi, W. Timp
- Biology, Medicine
- Nature Methods
- 1 April 2017
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford… Expand
Trait Variation in Yeast Is Defined by Population History
A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific… Expand
Efficient construction of an assembly string graph using the FM-index
We use suffix array-based methods that have formed the basis of recent very fast sequence mapping algorithms to find overlaps and generate assembly string graphs asymptotically faster than previously described algorithms. Expand
Real-time, portable genome sequencing for Ebola surveillance
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to… Expand