Results 21 to 30 of about 3,685 (173)

Succinct dynamic de Bruijn graphs [PDF]

Bioinformatics, 2020
Abstract Motivation The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. In order to be applicable to population-scale studies, it is essential to build and store the graph in a space- and time-efficient manner.
Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher 0001   +4 more
openaire   +3 more sources

Clover: a clustering-oriented de novo assembler for Illumina sequences

BMC Bioinformatics, 2020
Background Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers.
Ming-Feng Hsieh, Chin Lung Lu, Chuan Yi Tang   +2 more
doaj   +1 more source

Computing Genomic Signatures Using de Bruijn Chains

Advances in Computing and Engineering, 2021
Genomic DNA sequences have both deterministic and random aspects and exhibit features at numerous scales, from codons to regions of conserved or divergent gene order.
Lenwood S. Heath, Amrita Pati
doaj   +1 more source

Read mapping on de Bruijn graphs [PDF]

BMC Bioinformatics, 2016
Abstract Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig describes the sequence found along some path of the assembly graph, however, the
Limasset, Antoine, Cazaux, Bastien, Rivals, Eric, Peterlongo, Pierre   +3 more
openaire   +5 more sources

Sequence-based pangenomic core detection

iScience, 2022
Summary: One of the most basic kinds of analysis to be performed on a pangenome is the detection of its core, i.e., the information shared among all members. Pangenomic core detection is classically done on the gene level and many tools focus exclusively
Tizian Schulz, Roland Wittler, Jens Stoye   +2 more
doaj   +1 more source

Succinct Colored de Bruijn Graphs [PDF]

Bioinformatics, 2016
Abstract Iqbal et al. (Nature Genetics, 2012) introduced the colored de Bruijn graph , a variant of the classic de Bruijn graph, which is aimed at “detecting and genotyping simple and complex genetic variants in an individual or population”.
Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher 0001   +8 more
openaire   +2 more sources

MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly

BMC Bioinformatics, 2021
Background The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions.
Kuo-ching Liang, Yasubumi Sakakibara
doaj   +1 more source

DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage

Computational and Structural Biotechnology Journal, 2023
DNA is a high-density, long-term stable, and scalable storage medium that can meet the increased demands on storage media resulting from the exponential growth of data. The existing DNA storage encoding schemes tend to achieve high-density storage but do
Yunzhu Zhao, Ben Cao, Penghao Wang, Kun Wang, Bin Wang   +4 more
doaj   +1 more source

RResolver: efficient short-read repeat resolution within ABySS

BMC Bioinformatics, 2022
Background De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes.
Vladimir Nikolić, Amirhossein Afshinfard, Justin Chu, Johnathan Wong, Lauren Coombe, Ka Ming Nip, René L. Warren, Inanç Birol   +7 more
doaj   +1 more source

Covering the de Bruijn graph

Discrete Mathematics, 1991
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Roy D. Bryant, Harold Fredricksen
openaire   +2 more sources