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BIOINFORMATICS Genes and Genomes The fragment assembly string graph

by Eugene W. Myers
"... We present a concept and formalism, the string graph, which represents all that is inferable about a DNA sequence from a collection of shotgun sequencing reads collected from it. We give time and space efficient algorithms for constructing a string graph given the collection of overlaps between the ..."
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to the unitig approach we developed at Celera. This paper is a preliminary piece giving the basic algorithm and results that demonstrate the efficiency and scalability of the method. These ideas are being used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler

Strain-specific polymorphisms in Paneth cell alpha-defensins of C57BL/6 mice and evidence of vestigial myeloid alpha-defensin pseudogenes

by Michael T. Shanahan, Hiroki Tanabe, Andre ́ J. Ouellette - Infect. Immun
"... Paneth cells at the base of small intestinal crypts secrete microbicidal -defensins, termed cryptdins (Crps) in mice, as mediators of innate immunity. Proteomic studies show that five abundant Paneth cell -defensins in C57BL/6 mice are strain specific in that they have not been identified in other i ..."
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inbred strains of mice. Two C57BL/6-specific peptides are coded for by the Defcr20 and-21 genes evident in the NIH C57BL/6 genome but absent from the Celera mixed-strain assembly, which excludes C57BL/6 data and differs from the NIH build with respect to the organization of the -defensin gene locus

Highly Scalable Genome Assembly on Campus Grids

by Christopher Moretti, Michael Olson, Scott Emrich, Douglas Thain
"... Bioinformatics researchers need efficient means to process large collections of sequence data. One application of interest, genome assembly, has great potential for parallelization, however most previous attempts at parallelization require uncommon high-end hardware. This paper introduces a scalable ..."
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scalable modular genome assembler that can achieve significant speedup using large numbers of conventional desktop machines, such as those found in a campus computing grid. The system is based on the Celera open-source assembly toolkit, and replaces two independent sequential modules with scalable

unknown title

by unknown authors
"... editorial ENU mutagenesis: a work in progress Recent progress in the development of resources for genomic analysis, highlighted by the release of both proprietary (Celera) and public domain assemblies of the mouse genome ..."
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editorial ENU mutagenesis: a work in progress Recent progress in the development of resources for genomic analysis, highlighted by the release of both proprietary (Celera) and public domain assemblies of the mouse genome

Pages 1–8 Design of a Compartmentalized Shotgun

by Assembler For The Human Genome, Daniel H. Huson, Knut Reinert, Saul A. Kravitz, Karin A, Art L. Delcher, Ian M. Dew, Mike Flanigan, Aaron L, Halpern Zhongwu Lai
"... Two different strategies for determining the human genome are currently being pursued: one is the “clone-byclone” approach, employed by the publicly funded project, and the other is the “whole genome shotgun assembler” approach, favored by researchers at Celera Genomics. An interim strategy employed ..."
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Two different strategies for determining the human genome are currently being pursued: one is the “clone-byclone” approach, employed by the publicly funded project, and the other is the “whole genome shotgun assembler” approach, favored by researchers at Celera Genomics. An interim strategy

PREPRINT: A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids

by Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott Emrich, Douglas Thain
"... Abstract—Bioinformatics researchers need efficient means to process large collections of genomic sequence data. One application of interest, genome assembly, has great potential for parallelization, however most previous attempts at parallelization require uncommon high-end hardware. This paper intr ..."
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introduces the Scalable Assembler at Notre Dame (SAND) framework that can achieve significant speedup using large numbers of commodity machines harnessed from clusters, clouds, and grids. SAND interfaces with the Celera open-source assembly toolkit, replacing two independent sequential modules with scalable

1 Genome Analysis Omega: an Overlap-graph de novo Assembler for Metagenomics

by Bahlul Haider, Tae-hyuk Ahn, Brian Bushnell, Juanjuan Chai, Alex Copeland, Chongle
"... Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (over-lap-graph metagenome assembler) was developed for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads ..."
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to three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD, and MetaVelvet), Omega provided comparable overall performance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison to Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a

Anatomical and Behavioral Evolution

by Francisco Prosdocimi, Daniela Bittencourt, Felipe Rodrigues Da Silva, Matias Kirst, Paulo C, Elibio L. Rech
"... Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate, ..."
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spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative

Genome analysis Advance Access publication June 19, 2014 Omega: an Overlap-graph de novo Assembler for Metagenomics

by Bahlul Haider, Tae-hyuk Ahn, Brian Bushnell, Juanjuan Chai, Alex Copel, Chongle Pan , 2014
"... Motivation: Metagenomic sequencing allows reconstruction of micro-bial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads u ..."
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with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega provided comparable overall per-formance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison with Celera on the MiSeq data-set, Omega provided more continuous assemblies overall using a

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies

by Miriam K. Konkel A, Jianxin Wang B, Ping Liang B, Mark A. Batzer A , 2006
"... Mobile elements represent a relatively new class of markers for the study of human evolution. Long interspersed elements (LINEs) belong to a group of retrotransposons comprising approximately 21 % of the human genome. Young LINE-1 (L1) elements that have integrated recently into the human genome can ..."
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can be polymorphic for insertion presence/absence in different human populations at particular chromosomal locations. To identify putative novel L1 insertion polymorphisms, we computationally compared two draft assemblies of the whole human genome (Public and Celera Human Genome assemblies). We
Results 11 - 20 of 25