Results 21 to 30 of about 4,886,903 (295)

Fast search of thousands of short-read sequencing experiments [PDF]

Nature Biotechnology, 2016
The amount of sequence information in public repositories is growing at a rapid rate. Although these data are likely to contain clinically important information that has not yet been uncovered, our ability to effectively mine these repositories is limited.
Solomon, Brad, Kingsford, Carl
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

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

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

Genome Analysis Methods using Long Read Nanopore Sequencing [PDF]

, 2021
Third-generation long-read technologies denote the latest progression in high throughput DNA and RNA sequence analysis. Complementing the widespread second-generation short-read platforms, long-read sequencing adds unique application opportunities by ...
Giesselmann, Pay, Gießelmann, P. ; https://orcid.org/   +1 more
core   +1 more source

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

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

Geoseq: a tool for dissecting deep-sequencing datasets [PDF]

, 2010
Gurtowski J, Cancio A, Shah H, et al. Geoseq: a tool for dissecting deep-sequencing datasets. BMC Bioinformatics. 2010;11(1): 506.Background Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the ...
Gurtowski, James, Sachidanandam, Ravi, Robert Homann, Shah Hardik, Chaya Levovitz, Ravi Sachidanandam, Hardik Shah, James Gurtowski, Cancio, Anthony, Levovitz Chaya, George Ajish, Cancio Anthony, Homann, Robert, Anthony Cancio, Shah, Hardik, Homann Robert, Levovitz, Chaya, Sachidanandam Ravi, Ajish George, George, Ajish, Gurtowski James   +20 more
core   +1 more source

HAT: de novo variant calling for highly accurate short-read and long-read sequencing data [PDF]

, 2023
MOTIVATION: de novo variant (DNV) calling is challenging from parent-child sequenced trio data. We developed H are A nd T ortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data.
Ng, Jeffrey K., Turner, Tychele N., Ng, Jeffrey K, Turner, Tychele N   +3 more
core   +1 more source

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