Results 1 to 10 of about 334,258 (285)
Reference-guided de novo assembly approach improves genome reconstruction for related species [PDF]
BMC Bioinformatics, 2017 Background The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions ...
Heidi E. L. Lischer, Kentaro K. Shimizu
doaj +3 more sources
Extreme Scale De Novo Metagenome Assembly [PDF]
SC18: International Conference for High Performance Computing, Networking, Storage and Analysis, 2018 Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big
Arndt, Bill +8 more
core +9 more sources
DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach. [PDF]
PLoS ONEIn optical genome mapping (OGM), large numbers of individual DNA maps-sequence-specific data series along single DNA molecules-are produced. Such individual maps have to be stitched together in a process called de novo OGM assembly in order to create ...
Albertas Dvirnas +8 more
doaj +2 more sources
State of the art
Human Genomics, 2010 Recent studies in human genomes have demonstrated the use of de novo assemblies to identify genetic variations that are difficult for mapping-based approaches.
Li Yingrui +3 more
doaj +4 more sources
Graph Theoretical Strategies in De Novo Assembly
IEEE Access, 2022 De novo genome assemblers assume the reference genome is unavailable, incomplete, highly fragmented, or significantly altered as in cancer tissues. Algorithms for de novo assembly have been developed to deal with and assemble a large number of short ...
Kimia Behizadi +2 more
doaj +3 more sources
Feature-by-feature--evaluating de novo sequence assembly. [PDF]
PLoS ONE, 2012 The whole-genome sequence assembly (WGSA) problem is among one of the most studied problems in computational biology. Despite the availability of a plethora of tools (i.e., assemblers), all claiming to have solved the WGSA problem, little has been done ...
Francesco Vezzi +2 more
doaj +4 more sources
Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets [PDF]
Bioinformatics and Biology InsightsDe novo assembly of transcriptomes from species without reference genome remains a common problem in functional genomics. While methods and algorithms for transcriptome assembly are continually being developed and published, the quality of de novo ...
Gonzalez Sergio Alberto +4 more
doaj +2 more sources
De novo genome assemblies of butterflies [PDF]
GigaScience, 2021 Abstract Background The availability of thousands of genomes has enabled new advancements in biology. However, many genomes have not been investigated for their quality. Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de ...
Emily A Ellis +2 more
openaire +2 more sources
Empirical evaluation of methods for de novo genome assembly [PDF]
PeerJ Computer Science, 2021 Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms.
Firaol Dida, Gangman Yi
doaj +2 more sources
Genome-scale de novo assembly using ALGA [PDF]
Bioinformatics, 2021 Abstract Motivation There are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage.
Sylwester Swat +7 more
openaire +2 more sources