Results 31 to 40 of about 308,842 (252)

Genomic sequence characteristics and the empiric accuracy of short-read sequencing [PDF]

, 2021
Abstract Background Short-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias, reduce the performance of variant calling using short-read alignment, but the loss in ...
Maximillian Marin, Roger Vargas, Michael Harris, Brendan Jeffrey, L. Elaine Epperson, David Durbin, Michael Strong, Max Salfinger, Zamin Iqbal, Irada Akhundova, Sergo Vashakidze, Valeriu Crudu, Alex Rosenthal, Maha Reda Farhat   +13 more
openaire   +1 more source

ABySS: A parallel assembler for short read sequence data [PDF]

Genome Research, 2009
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of ...
Jared T, Simpson, Kim, Wong, Shaun D, Jackman, Jacqueline E, Schein, Steven J M, Jones, Inanç, Birol   +5 more
openaire   +2 more sources

Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing

Frontiers in Genetics, 2023
The novel coronavirus disease 2019 (COVID-19) pandemic poses a serious public health risk. In this report, we present a modified sequencing workflow using short tiling (280bp) amplicons library preparation method paired with Illumina’s iSeq100 desktop ...
Lian Chye Winston Koh, Lian Chye Winston Koh, Yiqi Seow, Yiqi Seow, Kiat Whye Kong, Ming Li Lalita Lau, Shoban Krishna Kumar, Gabriel Yan, Chun Kiat Lee, Benedict Yan, Paul Anantharajah Tambyah, Shawn Hoon   +11 more
doaj   +1 more source

Leveraging Short-Read Sequencing to Explore the Genomics of Sepiolid Squid [PDF]

Integrative and Comparative Biology, 2021
Synopsis Due to their large size (∼3–5 Gb) and high repetitive content, the study of cephalopod genomes has historically been problematic. However, with the recent sequencing of several cephalopod genomes, including the Hawaiian bobtail squid (Euprymna scolopes), whole-genome studies of these molluscs are now possible.
Elizabeth Heath-Heckman, Michele K Nishiguchi   +1 more
openaire   +2 more sources

Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Brucella melitensis Isolates

Microorganisms, 2022
Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis.
Hillary A. Craddock, Yair Motro, Bar Zilberman, Boris Khalfin, Svetlana Bardenstein, Jacob Moran-Gilad   +5 more
doaj   +1 more source

Assembling genomes using short-read sequencing technology [PDF]

Genome Biology, 2010
Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark.
Jackman, Shaun D, Birol, İnanç
openaire   +2 more sources

A sensitive short read homology search tool for paired-end read sequencing data

BMC Bioinformatics, 2017
Background Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species.
Prapaporn Techa-Angkoon, Yanni Sun, Jikai Lei   +2 more
doaj   +1 more source

Short Read (Next-Generation) Sequencing [PDF]

Circulation: Cardiovascular Genetics, 2013
Rapid advances in DNA sequencing technologies have made it increasingly cost-effective to obtain accurate and timely large-scale genomic sequence data on individuals (short read massively parallel or next generation [next-gen]). A next-gen molecular diagnostic approach that has seen rapid deployment in the clinic over the last year is exome sequencing.
Jaya, Punetha, Eric P, Hoffman
openaire   +2 more sources

A Review on Sequence Alignment Algorithms for Short Reads Based on Next-Generation Sequencing [PDF]

IEEE Access, 2020
With recent advances in next-generation sequencing (NGS) technology, large volumes of data have been produced in the form of short reads. Sequence assembly involves using initial short reads to produce progressively longer contigs, and then using scaffolds to produce the final sequence.
Jeongkyu Kim, Mingeun Ji, Gangman Yi
openaire   +2 more sources

Sequencing of natural strains of Arabidopsis thaliana with short reads [PDF]

Genome Research, 2008
Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis thaliana can differ by several percent of their sequence. To examine this variation, and as a first step in the 1001 Genomes Project for this species, we produced 15- to ...
Ossowski, Stephan, Schneeberger, Korbinian, Clark, Richard M, Lanz, Christa, Warthmann, Norman, Weigel, Detlef   +5 more
openaire   +4 more sources