21 Result(s)
within
English
Life Sciences
Animal Genetics and Genomics
Plant Genetics and Genomics
Adam M Phillippy
Article
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Open AccessFalse gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as com...
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Open AccessAuthor Correction: Improved reference genome of the arboviral vector Aedes albopictus
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Open AccessComplete vertebrate mitogenomes reveal widespread repeats and gene duplications
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
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Open AccessMerqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation...
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Open AccessImproved reference genome of the arboviral vector Aedes albopictus
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 a...
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Open AccessNew insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific g...
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Open AccessMash Screen: high-throughput sequence containment estimation for genome discovery
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. H...
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Open AccessAssignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read ...
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Open AccessRefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present t...
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Open AccessMash: fast genome and metagenome distance estimation using MinHash
Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mas...
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Open AccessThe Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequence...
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Open AccessReducing assembly complexity of microbial genomes with single-molecule sequencing
The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant r...
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Open AccessMetAMOS: a modular and open source metagenomic assembly and analysis pipeline
We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequ...
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Open AccessThe 15th Genomic Standards Consortium meeting
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Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone
A growing resource of methicillin-resistant Staphylococcus aureus (MRSA) genomes uncovers intriguing phylogeographic and recombination patterns and highlights challenges in identifying the source of these phenome...
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Open AccessGenomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity
Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study e...
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Open AccessProbing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultativ...
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Open AccessErratum to: Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
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Open AccessGenome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome se...
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Open AccessGenome assembly forensics: finding the elusive mis-assembly
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated...
