New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads
Sign Up to like & getrecommendations! Published in 2022 at "Life Science Alliance"
DOI: 10.1101/2022.08.30.505891
Abstract: Innovative algorithmic approaches were used to perform assembly of complex genomes across the tree of life, from long DNA sequencing data. Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA… read more here.
Keywords: new algorithms; sequencing reads; algorithms accurate; long dna ... See more keywords
De Novo Genome Sequencing, Annotation, and Taxonomy of Unknown Bacteria.
Sign Up to like & getrecommendations! Published in 2022 at "Cold Spring Harbor protocols"
DOI: 10.1101/pdb.top107847
Abstract: Whole-genome sequencing of viruses and bacteria has become routine thanks to advances in DNA-sequencing technologies. Parallel advances in computing power and software design allow for billions of base pairs of sequence information to be analyzed… read more here.
Keywords: unknown bacteria; annotation taxonomy; genome sequencing; taxonomy unknown ... See more keywords
SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
Sign Up to like & getrecommendations! Published in 2022 at "BMC Research Notes"
DOI: 10.1186/s13104-022-05978-5
Abstract: Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift… read more here.
Keywords: snakecube containerized; genome assembly; hpc; pipeline ... See more keywords
The long reads ahead: de novo genome assembly using the MinION
Sign Up to like & getrecommendations! Published in 2017 at "F1000Research"
DOI: 10.12688/f1000research.12012.2
Abstract: Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review… read more here.
Keywords: novo genome; reads ahead; assembly; ahead novo ... See more keywords
A de novo genome assembly of cultivated Prunus persica cv. ‘Sovetskiy’
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0269284
Abstract: Prunus persica is one of the main stone fruit crops in Crimea and southern Russia. The P. persica genome has recently been sequenced and annotated in good quality. However, for a deeper assessment of the… read more here.
Keywords: prunus persica; genome; persica sovetskiy; novo genome ... See more keywords
De Novo Genome Assembly of Auanema Melissensis, a Trioecious Free-Living Nematode
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Nematology"
DOI: 10.2478/jofnem-2022-0059
Abstract: Abstract Nematodes of the genus Auanema are interesting models for studying sex determination mechanisms because their populations consist of three sexual morphs (males, females, and hermaphrodites) and produce skewed sex ratios. Here, we introduce a… read more here.
Keywords: genome assembly; auanema melissensis; novo genome; melissensis ... See more keywords
Empirical evaluation of methods for de novo genome assembly
Sign Up to like & getrecommendations! Published in 2021 at "PeerJ Computer Science"
DOI: 10.7717/peerj-cs.636
Abstract: 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. A drastic reduction in the costs of generating short reads on the… read more here.
Keywords: empirical evaluation; novo genome; assembly algorithms; evaluation methods ... See more keywords