Results 21 to 30 of about 487,788 (325)

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

PLoS Computational Biology, 2018
Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective for small genomes.
Ryan R Wick, Louise M Judd, Kathryn E Holt   +2 more
doaj   +2 more sources

Methods for safely sharing dual-use genetic data [PDF]

Frontiers in Microbiology
BackgroundSome genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic.
Sterling Sawaya, Chien-Chi Lo, Po-E Li, Blake Hovde, Patrick Chain   +4 more
doaj   +2 more sources

Grenepipe: a Flexible, Scalable and Reproducible Pipeline to Automate Variant Calling from Sequence Reads [PDF]

Bioinform., 2021
SUMMARY We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls.
Lucas Czech, Moises Exposito-Alonso
semanticscholar   +1 more source

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

Frontiers in Bioinformatics, 2023
Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments.
Fotis A. Baltoumas, E. Karatzas, David Páez-Espino, N. K. Venetsianou, Eleni Aplakidou, A. Oulas, R. Finn, S. Ovchinnikov, E. Pafilis, N. Kyrpides, Georgios A. Pavlopoulos   +10 more
semanticscholar   +1 more source

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Scientific Reports, 2021
Third-generation sequencing technologies allow to sequence long reads of tens of kbp, that are expected to solve various problems. However, they display high error rates, currently capped around 10%.
Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre   +4 more
doaj   +1 more source

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA)

PeerJ, 2023
Background The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species.
Genki Kobayashi
semanticscholar   +1 more source

De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening [PDF]

Archives of Biological Sciences, 2017
Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L.
Peng Yong, Ma Huiqin, Chen Shangwu
doaj   +1 more source

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

bioRxiv, 2023
Background  PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes.
Marcela Uliano-Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, G. Formenti, Linelle Abueg, J. Torrance, Eugene W. Myers, R. Durbin, Mark Blaxter, Shane A. McCarthy   +9 more
semanticscholar   +1 more source

RNA-seq data from C-X-C chemokine receptor type 5 (CXCR5) gene knockout aged mice with retinal degeneration phenotype

Data in Brief, 2020
The CXCR5 (C-X-C motif chemokine receptor 5) is chemokine transmembrane receptor, acting via its ligand CXCL13 and plays a crucial role in controlling the trafficking of inflammatory cells into and from the sub-retinal space, which contributes to the ...
Madhu Sudhana Saddala, Anton Lennikov, Hu Huang   +2 more
doaj   +1 more source

The complete genome sequence of Stevia rebaudiana, the Sweetleaf [version 1; peer review: 2 approved, 1 approved with reservations]

F1000Research, 2020
The Sweetleaf (Stevia rebaudiana: Asteraceae) is widely grown for use as a sweetener.  We present the whole genome sequence and annotation of this species.  A total of 146,838,888 paired-end reads consisting of 22.2G bases were obtained by sequencing one
Kathleen O'Neill, Stacy Pirro
doaj   +1 more source