Results 21 to 30 of about 225,232 (252)

kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on the K-Mer Neighborhood Graph

Frontiers in Genetics, 2022
With the rapid development of single molecular sequencing (SMS) technologies such as PacBio single-molecule real-time and Oxford Nanopore sequencing, the output read length is continuously increasing, which has dramatical potentials on cutting-edge ...
Ze-Gang Wei, Xing-Guo Fan, Hao Zhang, Xiao-Dan Zhang, Fei Liu, Yu Qian, Shao-Wu Zhang   +6 more
doaj   +1 more source

smsMap: mapping single molecule sequencing reads by locating the alignment starting positions

BMC Bioinformatics, 2020
Background Single Molecule Sequencing (SMS) technology can produce longer reads with higher sequencing error rate. Mapping these reads to a reference genome is often the most fundamental and computing-intensive step for downstream analysis. Most existing
Ze-Gang Wei, Shao-Wu Zhang, Fei Liu
doaj   +1 more source

Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster

G3: Genes, Genomes, Genetics, 2018
Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing
Evan Long, Carrie Evans, John Chaston, Joshua A. Udall   +3 more
doaj   +1 more source

Long-read single-molecule maps of the functional methylome [PDF]

Genome Research, 2019
We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs.
Hila Sharim, Assaf Grunwald, Tslil Gabrieli, Yael Michaeli, Sapir Margalit, Dmitry Torchinsky, Rani Arielly, Gil Nifker, Matyas Juhasz, Felix Gularek, Miguel Almalvez, Brandon Dufault, Sreetama Sen Chandra, Alexander Liu, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Kathryn R. Wagner, Jonathan Pevsner, Jeff Reifenberger, Ernest T. Lam, Alex R. Hastie, Han Cao, Hayk Barseghyan, Elmar Weinhold, Yuval Ebenstein   +25 more
openaire   +5 more sources

Nanopore sequencing unveils the complexity of the cold-activated murine brown adipose tissue transcriptome

iScience, 2023
Summary: Alternative transcription increases transcriptome complexity by expression of multiple transcripts per gene. Annotation and quantification of transcripts using short-read sequencing is non-trivial.
Christoph Andreas Engelhard, Sajjad Khani, Sophia Derdak, Martin Bilban, Jan-Wilhelm Kornfeld   +4 more
doaj   +1 more source

S-conLSH: alignment-free gapped mapping of noisy long reads [PDF]

BMC Bioinformatics, 2019
Abstract Background The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective reference genome is the first but costliest step of any analysis pipeline
Chakraborty, Angana, Morgenstern, Burkhard, Bandyopadhyay, Sanghamitra, Chakraborty, Angana; Department of Computer Science, West Bengal Education Service, Kolkata, India, Morgenstern, Burkhard; Department of Bioinformatics (IMG), University of Göttingen, Göttingen, Germany, Bandyopadhyay, Sanghamitra; Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India   +5 more
openaire   +5 more sources

Structural variant calling: the long and the short of it

Genome Biology, 2019
Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution—giving ...
Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz, Fritz J. Sedlazeck   +5 more
doaj   +1 more source

Efficient mapping of accurate long reads in minimizer space with mapquik

Genome Research, 2023
DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (e.g., Pacific Biosciences [PacBio] HiFi) to a reference genome, which poses challenges in terms of accuracy and ...
Bariş Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi   +4 more
openaire   +4 more sources

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Nature Communications, 2016
Read mapping and alignment tools are critical for many applications based on MinION sequencers. Here, the authors present GraphMap, a mapping algorithm designed to analyze nanopore sequencing reads, that progressively refines candidate alignments to ...
Ivan Sović, Mile Šikić, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen, Niranjan Nagarajan   +5 more
doaj   +1 more source

RASSA: Resistive Prealignment Accelerator for Approximate DNA Long Read Mapping [PDF]

IEEE Micro, 2019
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive approximate similarity search accelerator, RASSA, exploits charge distribution and parallel in-memory processing to ...
Kaplan, Roman, Yavits, Leonid, Ginosar, Ran   +2 more
openaire   +2 more sources