Results 41 to 50 of about 4,886,903 (295)

A comprehensive evaluation of alignment algorithms in the context of RNA-seq. [PDF]

, 2012
Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level.
Friedel, Caroline C., Friedel Caroline C., Caroline C. Friedel (29226), Caroline C Friedel, Lindner, Robert, Lindner Robert, Robert Lindner (107994), Robert Lindner, Caroline C. Friedel   +8 more
core   +2 more sources

Merging short and stranded long reads improves transcript assembly.

PLoS Computational Biology, 2023
Long-read RNA sequencing has arisen as a counterpart to short-read sequencing, with the potential to capture full-length isoforms, albeit at the cost of lower depth.
Amoldeep S Kainth, Gabriela A Haddad, Johnathon M Hall, Alexander J Ruthenburg   +3 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

From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes [PDF]

, 2014
Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA
Matisoo-Smith, Elizabeth A, Soria Hernanz, David F, Schurr, Theodore G., Stanton, Jo-Ann, Martínez-Cruz, Begoña, White, W. T., GaneshPrasad, Arun Kumar, Lacerda, Daniela R., Matisoo Smith, Elizabeth, White, W. Timothy J., Vilar, Miguel G., Platt, Daniel E., Parida, Laxmi, Hernanz, Soria, Martínez Cruz, Begoña, Kaplan, Matthew E., Clarke, Andrew, Schurr, Theodore G, Matisoo-Smith, Lisa, Matisoo-Smith, Elizabeth, Mitchell, R. John, Matthew E Kaplan, Vieira, Pedro Paulo, Jo-Ann L Stanton, Matisoo-Smith, Elizabeth A., Dulik, Matthew C., Zalloua, Pierre A., Kaplan, Matthew, Tyler-Smith, Chris, Kaplan, M., W Timothy J White, Santhakumari, Arun Varatharajan, Haak, Wolfgang, Quintana-Murci, Lluis, Stefan Prost, null null, Comas, David, Ziegle, Janet S., Swamikrishnan, Pandikumar, Kaplan, Matthew E, Wells, R. Spencer, HASH(0x55a67fb2a340), White, W Timothy J, Cooper, Alan, Clarke, Andrew C, Der Sarkissian, Clio S.I., The, Genographic Consortium, Stanton, J., Bertranpetit, Jaume, 1952-, White, W Timothy J., Stanton, Jo-Ann L., Stanton, Jo Ann L., Pitchappan, Ramasamy, Adhikarla, Syama, Santos, Fabrício R., Comas, David, 1969-, Haber, Marc; id_orcid, Soodyall, Himla, Royyuru, Ajay K., Prost, Stefan, Adler, Christina J., Renfrew, Colin, Jin, Li, Clark, Andrew, Elizabeth A Matisoo-Smith, Andrew C Clarke, Matisoo-Smith, E., Li, Shilin, The Genographic Consortium, Balanovsky, Oleg, Balanovska, Elena, Clarke, Andrew C., Prost, S., Merchant, Nirav C., Andrew C Clarke, Owings, Amanda C., Stanton, Jo-Ann L, White, W., Bertranpetit, Jaume, Gaieski, Jill B., Genographic Consortium, Haber, Marc, 1980-, Genographic Consortium,, Clarke, A.   +83 more
core   +1 more source

Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

Molecular Genetics & Genomic Medicine, 2020
Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by ...
Kévin Uguen, Claire Jubin, Yannis Duffourd, Claire Bardel, Valérie Malan, Jean‐Michel Dupont, Laila El Khattabi, Nicolas Chatron, Antonio Vitobello, Pierre‐Antoine Rollat‐Farnier, Céline Baulard, Marc Lelorch, Aurélie Leduc, Emilie Tisserant, Frédéric Tran Mau‐Them, Vincent Danjean, Marc Delepine, Marianne Till, Vincent Meyer, Stanislas Lyonnet, Anne‐laure Mosca‐Boidron, Julien Thevenon, Laurence Faivre, Christel Thauvin‐Robinet, Caroline Schluth‐Bolard, Anne Boland, Robert Olaso, Patrick Callier, Serge Romana, Jean‐François Deleuze, Damien Sanlaville   +30 more
doaj   +1 more source

Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

BMC Genomics, 2021
Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis.
Kerstin Neubert, Eric Zuchantke, Robert Maximilian Leidenfrost, Roebbe Wuenschiers, Josephine Grützke, Burkhard Malorny, Holger Brendebach, Sascha Al Dahouk, Timo Homeier, Helmut Hotzel, Knut Reinert, Herbert Tomaso, Anne Busch   +12 more
doaj   +1 more source

Software for pre-processing Illumina next-generation sequencing short read sequences [PDF]

Source Code for Biology and Medicine, 2014
When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g.
Chuming Chen, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu   +3 more
openaire   +3 more sources

Linked-read sequencing for detecting short tandem repeat expansions

Scientific Reports, 2022
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences.
Readman Chiu, Indhu-Shree Rajan-Babu, Inanc Birol, Jan M. Friedman   +3 more
doaj   +1 more source

Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data [PDF]

The American Journal of Human Genetics, 2018
Repeat expansions cause more than 30 inherited disorders, predominantly neurogenetic. These can present with overlapping clinical phenotypes, making molecular diagnosis challenging. Single-gene or small-panel PCR-based methods can help to identify the precise genetic cause, but they can be slow and costly and often yield no result.
Tankard, R.M., Bennett, M.F., Degorski, P., Delatycki, M.B., Lockhart, P.J., Bahlo, M.   +5 more
openaire   +2 more sources

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis [PDF]

, 2010
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing.
Kück Ulrich, Espagne, Eric, Jason E Stajich, Kempken, Frank, Ines Engh, Stefanie Pöggeler, Frank Kempken, Ulrich Kück, Kuo, Hsiao Che, Jens Kamerewerd, Osiewacz, Heinz D., Zickler, Denise, Espagne Eric, Kück, Ulrich, Engh Ines, Freitag, Michael H., Smith, Kristina M, Meiling Chu, Chu Meiling, Smith Kristina M., Kuo, Hsiao-Che, Read, Nick D, Heinz D Osiewacz, Kempken Frank, Poeggeler, Stefanie, Knab, Birgit, Birgit Knab, Denise Zickler, Kuo Hsiao-Che, Kueck, Ulrich, Stajich Jason E., Osiewacz, Heinz D, Stajich, Jason E, Michael Freitag, Stephan Seiler, Halliday, Karen, Freitag, Michael, Stajich, Jason E., Chu, Meiling, Nick D Read, Karen Halliday, Knab Birgit, Zickler Denise, Kristina M Smith, Pöggeler, Stefanie, Engh, Ines, Eric Espagne, Hsiao-Che Kuo, Kamerewerd Jens, Smith, Kristina M., Halliday Karen, Pöggeler Stefanie, Seiler Stephan, Read Nick D., Nowrousian, Minou, Seiler, Stephan, Osiewacz Heinz D., Freitag Michael, Nowrousian Minou, Read, Nick D., Kamerewerd, Jens, Minou Nowrousian   +61 more
core   +2 more sources