Results 41 to 50 of about 1,311,956 (360)

BFC: correcting Illumina sequencing errors [PDF]

Bioinformatics, 2015
Abstract Summary: BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to ...
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Analyzing and minimizing bias in Illumina sequencing libraries [PDF]

Genome Biology, 2010
Although Illumina shot-gun reads cover most genomes almost completely, sequences with extreme base compositions are often underrepresented or missing. Bias can potentially be introduced at any step during the library construction in the lab, on the Illumina instrument, in data processing or at the sequence analysis stage.
Sheila Fisher, Wei-Shen Chen, Kristen M. Connolly, Carsten Russ, Michael G. Ross, David M. Jaffe, James Meldrim, Chad Nusbaum, Andreas Gnirke, Daniel Aird   +9 more
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Paragraph: a graph-based structural variant genotyper for short-read sequence data

Genome Biology, 2019
Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines.
Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M. Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David R. Bentley, Michael C. Schatz, Fritz J. Sedlazeck, Michael A. Eberle   +10 more
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Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

BMC Genomics, 2023
Background The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two
Iamshchikov Pavel, Larionova Irina, Gerashchenko Tatiana, Piankov Denis, Koshkin Philipp, Korostelev Sergei, Denisov Evgeny   +6 more
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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification [PDF]

, 2020
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a ...
Barton, Geoffrey J., Gould, Peter D., Hall, Anthony J. W., Knop, Katarzyna, Mackinnon, Katarzyna, Parker, Matthew T., Schurch, Nicholas J., Sherwood, Anna V., Simpson, Gordon G.   +8 more
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Complete Genome Sequence of Neisseria musculi Using Illumina and PacBio Sequencing

Microbiology Resource Announcements, 2021
Neisseria musculi is an oral commensal of wild-caught mice. Here, we report the complete genome sequence of N. musculi strain NW831, generated using a combination of the Illumina and PacBio platforms.
Eliza Thapa, Jain Aluvathingal, Suvarna Nadendla, Aditya Mehta, Hervé Tettelin, Nathan J. Weyand   +5 more
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A pilot study for channel catfish whole genome sequencing and de novo assembly

BMC Genomics, 2011
Background Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs.
Jiang Yanliang, Lu Jianguo, Peatman Eric, Kucuktas Huseyin, Liu Shikai, Wang Shaolin, Sun Fanyue, Liu Zhanjiang   +7 more
doaj   +1 more source

Despite low viral titer in saliva samples, Sanger-based SARS-CoV-2 spike gene sequencing is highly applicable for the variant identification

BMC Medical Genomics, 2023
Background This study aimed to compare the performance of Sanger-based SARS-CoV-2 spike gene sequencing and Next Generation Sequencing (NGS)-based full-genome sequencing for variant identification in saliva samples with low viral titer. Methods Using 241
Ko Ko, Kazuaki Takahashi, Noriaki Ito, Aya Sugiyama, Shintaro Nagashima, Kei Miwata, Yoshihiro Kitahara, Mafumi Okimoto, Serge Ouoba, Golda Ataa Akuffo, Bunthen E, Tomoyuki Akita, Toshiro Takafuta, Junko Tanaka   +13 more
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German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing

Frontiers in Microbiology, 2020
We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria ...
Laura Uelze, Maria Borowiak, Markus Bönn, Erik Brinks, Carlus Deneke, Thomas Hankeln, Sylvia Kleta, Larissa Murr, Kerstin Stingl, Kathrin Szabo, Simon H. Tausch, Anne Wöhlke, Burkhard Malorny   +12 more
doaj   +1 more source

Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene [PDF]

Scientific Reports, 2016
AbstractGreen fluorescent protein (GFP) is one of the most used reporter genes. We have used next-generation sequencing (NGS) to analyse the genetic diversity of a recombinant influenza A virus that expresses GFP and found a remarkable coverage dip in the GFP coding sequence.
Van den Hoecke, Silvie, Verhelst, Judith, Saelens, Xavier   +2 more
openaire   +4 more sources