15 Result(s)

Article

False 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...

Juwan Kim, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won… in Genome Biology (2022)

Article

Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren… in Genome Biology (2021)

Article

Complete 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.

Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase… in Genome Biology (2021)

Article

Merqury: 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...

Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy in Genome Biology (2020)

Article

Improved 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...

Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren… in Genome Biology (2020)

Article

Mash 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...

Brian D. Ondov, Gabriel J. Starrett, Anna Sap**ton, Aleksandra Kostic… in Genome Biology (2019)

Article

Assignment 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 ...

Derek M. Bickhart, Mick Watson, Sergey Koren, Kevin Panke-Buisse… in Genome Biology (2019)

Article

RefSeq 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...

Daniel J. Nasko, Sergey Koren, Adam M. Phillippy, Todd J. Treangen in Genome Biology (2018)

Article

Mash: 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...

Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee… in Genome Biology (2016)

Article

The 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...

Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M Phillippy in Genome Biology (2014)

Article

Reducing 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...

Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono… in Genome Biology (2013)

Article

MetAMOS: 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...

Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya… in Genome Biology (2013)

Article

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...

Todd J Treangen, Adam M Phillippy in Genome Biology (2012)

Article

Genome 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...

Adam M Phillippy, Michael C Schatz, Mihai Pop in Genome Biology (2008)

Article

Hawkeye: an interactive visual analytics tool for genome assemblies

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to...

Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg in Genome Biology (2007)