GAGE: A critical evaluation of genome assemblies and assembly algorithms
New sequencing technology has dramatically altered the landscape of whole-genome
sequencing, allowing scientists to initiate numerous projects to decode the genomes of …
sequencing, allowing scientists to initiate numerous projects to decode the genomes of …
Assembly of long error-prone reads using de Bruijn graphs
Y Lin, J Yuan, M Kolmogorov… - Proceedings of the …, 2016 - National Acad Sciences
The recent breakthroughs in assembling long error-prone reads were based on the overlap-
layout-consensus (OLC) approach and did not utilize the strengths of the alternative de …
layout-consensus (OLC) approach and did not utilize the strengths of the alternative de …
[HTML][HTML] Insights into hominid evolution from the gorilla genome sequence
Gorillas are humans' closest living relatives after chimpanzees, and are of comparable
importance for the study of human origins and evolution. Here we present the assembly and …
importance for the study of human origins and evolution. Here we present the assembly and …
Identification of novel transcripts in annotated genomes using RNA-Seq
We describe a new 'reference annotation based transcript assembly'problem for RNA-Seq
data that involves assembling novel transcripts in the context of an existing annotation. This …
data that involves assembling novel transcripts in the context of an existing annotation. This …
[HTML][HTML] The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous
economic value. Here we report a high-quality reference genome sequence of channel …
economic value. Here we report a high-quality reference genome sequence of channel …
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen
detection in the clinical microbiology laboratory and have numerous applications for public …
detection in the clinical microbiology laboratory and have numerous applications for public …
Applications of next-generation sequencing to phylogeography and phylogenetics
This is a time of unprecedented transition in DNA sequencing technologies. Next-generation
sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus …
sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus …
New approaches for metagenome assembly with short reads
M Ayling, MD Clark, RM Leggett - Briefings in bioinformatics, 2020 - academic.oup.com
In recent years, the use of longer range read data combined with advances in assembly
algorithms has stimulated big improvements in the contiguity and quality of genome …
algorithms has stimulated big improvements in the contiguity and quality of genome …
[HTML][HTML] Taming the beast: a revised classification of Cortinariaceae based on genomic data
Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest
Agaricales genus, with thousands of species worldwide. The species are important …
Agaricales genus, with thousands of species worldwide. The species are important …
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
Snakes are limbless predators, and many species use venom to help overpower relatively
large, agile prey. Snake venoms are complex protein mixtures encoded by several …
large, agile prey. Snake venoms are complex protein mixtures encoded by several …