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Maximum Likelihood Genome Assembly [PDF]
Journal of Computational Biology, 2009 Whole genome shotgun assembly is the process of taking many short sequenced segments (reads) and reconstructing the genome from which they originated. We demonstrate how the technique of bidirected network flow can be used to explicitly model the double-stranded nature of DNA for genome assembly.
Paul, Medvedev, Michael, Brudno
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B-assembler: a circular bacterial genome assembler
BMC Genomics, 2022 Abstract Background Accurate bacteria genome de novo assembly is fundamental to understand the evolution and pathogenesis of new bacteria species. The advent and popularity of Third-Generation Sequencing (TGS) enables assembly of bacteria genomes at an unprecedented speed. However, most current
Fengyuan Huang +7 more
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Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. [PDF]
PLoS ONE, 2013 A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently.
Dimitrios Kleftogiannis +2 more
doaj +1 more source
BMC Research Notes, 2023 Objective The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America.
O. P. Perera +10 more
doaj +1 more source
Are we there yet? : reliably estimating the completeness of plant genome sequences [PDF]
, 2016 Genome sequencing is becoming cheaper and faster thanks to the introduction of next-generation sequencing techniques. Dozens of new plant genome sequences have been released in recent years, ranging from small to gigantic repeat-rich or polyploid genomes.
Ruttink, Tom +2 more
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Improved reference genome of the arboviral vector Aedes albopictus [PDF]
, 2020 Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito ...
Akbari, Omar, +30 more
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Whole-genome shotgun assembly and comparison of human genome assemblies [PDF]
Proceedings of the National Academy of Sciences, 2004 We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and
Istrail, S. +35 more
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BlobTools: Interrogation of genome assemblies [PDF]
F1000Research, 2017 The goal of many genome sequencing projects is to provide a complete representation of a target genome (or genomes) as underpinning data for further analyses. However, it can be problematic to identify which sequences in an assembly truly derive from the target genome(s) and which are derived from associated microbiome or contaminant organisms.
Dominik R. Laetsch, Mark L. Blaxter
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Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing. [PDF]
, 2015 Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits.
Glazer, Andrew M +4 more
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De novo assembly of the cattle reference genome with single-molecule sequencing. [PDF]
, 2020 BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated ...
Bickhart, Derek M +32 more
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