Results 11 to 20 of about 566,210 (290)

Unlocking short read sequencing for metagenomics.

PLoS ONE, 2010
BackgroundDifferent high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.Methodology/principal ...
Sébastien Rodrigue, Arne C Materna, Sonia C Timberlake, Matthew C Blackburn, Rex R Malmstrom, Eric J Alm, Sallie W Chisholm   +6 more
doaj   +6 more sources

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing. [PDF]

PLoS ONE, 2016
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences.
James A Stapleton, Jeongwoon Kim, John P Hamilton, Ming Wu, Luiz C Irber, Rohan Maddamsetti, Bryan Briney, Linsey Newton, Dennis R Burton, C Titus Brown, Christina Chan, C Robin Buell, Timothy A Whitehead   +12 more
doaj   +6 more sources

Deconvolute individual genomes from metagenome sequences through short read clustering. [PDF]

PeerJ, 2020
Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of
Deng, Li, Li, Kexue, Lu, Yakang, Shi, Lizhen, Wang, Lili, Wang, Zhong   +5 more
core   +6 more sources

Estimation of Sequencing Error Rates in Short Reads [PDF]

BMC Bioinformatics, 2012
Background: Short-read data from next-generation sequencing technologies are now being generated across a range of research projects. The fidelity of this data can be affected by several factors and it is important to have simple and reliable approaches ...
Blades, Natalie, Ding, Jie, Parmigiani, Giovanni, Sultana, Razvan, Wang, Xin Victoria   +4 more
core   +7 more sources

Detection of trait-associated structural variations using short-read sequencing. [PDF]

Cell Genom, 2023
Genomic structural variation (SV) affects genetic and phenotypic characteristics in diverse organisms, but the lack of reliable methods to detect SV has hindered genetic analysis. We developed a computational algorithm (MOPline) that includes missing call recovery combined with high-confidence SV call selection and genotyping using short-read whole ...
Kosugi S, Kamatani Y, Harada K, Tomizuka K, Momozawa Y, Morisaki T, BioBank Japan Project, Terao C.   +7 more
europepmc   +3 more sources

Constructing a draft Indian cattle pangenome using short-read sequencing. [PDF]

Commun Biol
Abstract Indian desi cattle, known for their adaptability and phenotypic diversity, represent a valuable genetic resource. However, a single reference genome often fails to capture the full extent of their genetic variation. To address this, we construct a pangenome for
Azam S, Sahu A, Pandey NK, Neupane M, Van Tassell CP, Rosen BD, Gandham RK, Rath SN, Majumdar SS.   +8 more
europepmc   +4 more sources

Short read sequence typing (SRST): multi-locus sequence types from short reads [PDF]

BMC Genomics, 2012
Abstract Background Multi-locus sequence typing (MLST) has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven) to divide the population and is simple, robust and facilitates comparison of results between laboratories ...
Inouye, M, Conway, TC, Zobel, J, Holt, KE   +3 more
openaire   +4 more sources

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

Microindel detection in short-read sequence data [PDF]

Bioinformatics, 2010
Abstract Motivation: Several recent studies have demonstrated the effectiveness of resequencing and single nucleotide variant (SNV) detection by deep short-read sequencing platforms. While several reliable algorithms are available for automated SNV detection, the automated detection of microindels in deep short-read data presents a new ...
Krawitz, P., Rödelsperger, C., Jäger, M., Jostins, L., Bauer, S., Robinson, P.   +5 more
openaire   +4 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