Results 21 to 30 of about 399,495 (297)

A Sequence Distance Graph framework for genome assembly and analysis [version 1; peer review: 2 approved]

F1000Research, 2019
The Sequence Distance Graph (SDG) framework works with genome assembly graphs and raw data from paired, linked and long reads. It includes a simple deBruijn graph module, and can import graphs using the graphical fragment assembly (GFA) format.
Luis Yanes, Gonzalo Garcia Accinelli, Jonathan Wright, Ben J. Ward, Bernardo J. Clavijo   +4 more
doaj   +1 more source

High-coverage sequencing and annotated assemblies of the budgerigar genome [PDF]

, 2014
BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds.
Aboukhalil, R., Bukovnik, L., Fedrigo, O., Ganapathy, G., Howard, J. T., Jarvis, E. D., Knight, J. R., Koren, S., Li, B., Li, J., Li, Y., Phillippy, A. M., Rasolonjatovo, I., Schatz, M., Schwartz, D. C., Wang, T., Ward, J. M., Warren, W. C., Winer, R., Wray, G., Xiong, Y., Zhang, G., Zhang, Y., Zhou, S.   +23 more
core   +1 more source

MinION Analysis and Reference Consortium: Phase 1 data release and analysis [PDF]

, 2015
The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools.
Benedict Paten, Bonnie L. Brown, Camilla L.C. Ip, David A. Eccles, David Buck, Elizabeth M. Batty, Ewan Birney, Hans J. Jansen, Hugh E. Olsen, Jared T. Simpson, John M. Urban, John R. Tyson, Justin O'Grady, Mariateresa de Cesare, Matthew Loose, MinION Analysis and Reference Consortium, Miten Jain, Paolo Piazza, Richard M. Leggett, Rory J. Bowden, Sara Goodwin, Solomon Mwaigwisya, Terrance P. Snutch, Vadim Zalunin   +23 more
core   +2 more sources

De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys

Genomics Data, 2017
Monotropa hypopitys (pinesap) is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order
Alexey V. Beletsky, Mikhail A. Filyushin, Eugeny V. Gruzdev, Alexander M. Mazur, Egor B. Prokhortchouk, Elena Z. Kochieva, Andrey V. Mardanov, Nikolai V. Ravin, Konstantin G. Skryabin   +8 more
doaj   +1 more source

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing [PDF]

, 2016
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors
Decock, Anneleen, Ongenaert, Maté, Speleman, Franki, Van Criekinge, Wim, Vandesompele, Jo   +4 more
core   +1 more source

PacBio long read-assembled draft genome of Pythium insidiosum strain Pi-S isolated from a Thai patient with pythiosis

BMC Research Notes, 2023
Objectives Pythium insidiosum is the causative agent of pythiosis, a difficult-to-treat condition, in humans and animals worldwide. Biological information about this filamentous microorganism is sparse. Genomes of several P.
Theerapong Krajaejun, Preecha Patumcharoenpol, Thidarat Rujirawat, Weerayuth Kittichotirat, Sithichoke Tangphatsornruang, Tassanee Lohnoo, Wanta Yingyong   +6 more
doaj   +1 more source

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data

Journal of Computational Biology, 2023
The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the millions of samples of SARS-CoV-2 currently available, have appeared. Such a tool is tailored to take as input assembled,
Chourasia P., Ali S., Ciccolella S., Della Vedova G., Patterson M.   +4 more
openaire   +4 more sources

Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia

Data in Brief, 2018
We present raw sequence reads and genome assemblies derived from 17 accessions of the Ethiopian orphan crop plant enset (Ensete ventricosum (Welw.) Cheesman) using the Illumina HiSeq and MiSeq platforms. Also presented is a catalogue of single-nucleotide
Zerihun Yemataw, Sadik Muzemil, Daniel Ambachew, Leena Tripathi, Kassahun Tesfaye, Alemayheu Chala, Audrey Farbos, Paul O’Neill, Karen Moore, Murray Grant, David J. Studholme   +10 more
doaj   +1 more source

Whole genome sequencing data of Chromobacterium amazonense BASUSDA_45 isolated from soil in Bangladesh capable of degrading pesticide

Data in Brief, 2023
This article reports the Chromobacterium amazonense BASUSDA_45 strain's draft genomic sequence. The bacterium was isolated from cypermethrin pesticide contaminated soil and then the sequencing was carried out.
Md Atikur Rahman, Khaled Mahmud Sujon, Mohammad Tanbir Habib, Md. Forhad Hossain, K.M.K.B. Ferdaus, K.M.F. Hoque, Zennat Ferdousi, Md Abu Reza   +7 more
doaj   +1 more source

Shotgun metagenomic data of microbiomes on plastic fabrics exposed to harsh tropical environments

Data in Brief, 2020
The development of more affordable high-throughput DNA sequencing technologies and powerful bioinformatics is making of shotgun metagenomics a common tool for effective characterization of microbiomes and robust functional genomics. A shotgun metagenomic
Osman Radwan, Oscar N. Ruiz
doaj   +1 more source