Results 31 to 40 of about 327,413 (252)

Critical length in long-read resequencing [PDF]

NAR Genomics and Bioinformatics, 2019
Abstract Long-read sequencing has substantial advantages for structural variant discovery and phasing of variants compared to short-read technologies, but the required and optimal read length has not been assessed. In this work, we used long reads simulated from human genomes and evaluated structural variant discovery and variant phasing
Wouter, De Coster, Mojca, Strazisar, Peter, De Rijk   +2 more
openaire   +3 more sources

Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome, 2021
Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing.
Benjamin J. Callahan, Dmitry Grinevich, Siddhartha Thakur, Michael A. Balamotis, Tuval Ben Yehezkel   +4 more
doaj   +1 more source

Detecting haplotype-specific transcript variation in long reads with FLAIR2. [PDF]

Genome Biol
Background RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases.
Tang AD, Felton C, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN.   +5 more
europepmc   +2 more sources

S-conLSH: alignment-free gapped mapping of noisy long reads

BMC Bioinformatics, 2021
Background The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective reference genome is the first but ...
Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay   +2 more
doaj   +1 more source

Towards reliable whole genome sequencing for outbreak preparedness and response

BMC Genomics, 2022
Background To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making.
David F. Nieuwenhuijse, Anne van der Linden, Robert H. G. Kohl, Reina S. Sikkema, Marion P. G. Koopmans, Bas B. Oude Munnink   +5 more
doaj   +1 more source

Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution [PDF]

Frontiers in Genetics
Philipp Schiffer, Nadege Guiglielmoni, Joseph Kirangwa   +2 more
exaly   +2 more sources

Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing [PDF]

Plant Physiology, 2018
Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short- and long-read cDNA ...
David E. Cook, Jose Espejo Valle-Inclan, Alice Pajoro, Hanna Rovenich, Bart P.H.J. Thomma, Luigi Faino   +5 more
openaire   +2 more sources

Long-fragment targeted capture for long read sequencing of plastomes [PDF]

Applications in Plant Sciences, 2018
Third generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities to better study biodiversity, phylogeography and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to ...
Kevin Bethune, Cédric Mariac, Marie Couderc, Nora Scarcelli, Sylvain Santoni, Morgane Ardisson, Jean‐François Martin, Rommel Montúfar, Valentin Klein, François Sabot, Yves Vigouroux, Thomas L. P. Couvreur   +11 more
openaire   +8 more sources

Haplotype threading: accurate polyploid phasing from long reads

Genome Biology, 2020
Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies.
Sven D. Schrinner, Rebecca Serra Mari, Jana Ebler, Mikko Rautiainen, Lancelot Seillier, Julia J. Reimer, Björn Usadel, Tobias Marschall, Gunnar W. Klau   +8 more
doaj   +1 more source

phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

Genome Biology, 2021
Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly.
Xiao Luo, Xiongbin Kang, Alexander Schönhuth   +2 more
doaj   +1 more source