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. +4 more
openaire +4 more sources
SequelTools: a suite of tools for working with PacBio Sequel raw sequence data
BMC Bioinformatics, 2019 PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its real-time sequencing methodology.
David E. Hufnagel +2 more
semanticscholar +1 more source
BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis
Bioinform., 2020 Motivation High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially
Gianvito Urgese +4 more
semanticscholar +1 more source
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 +7 more
doaj +1 more source
Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples [PDF]
, 2015 Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the ...
Li, Heng
core +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
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus [PDF]
, 2014 As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death,
Eisen, Michael B, MacManes, Matthew D
core +4 more sources
Rapid and precise alignment of raw reads against redundant databases with KMA
BMC Bioinformatics, 2018 As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most ...
P. Clausen, F. Aarestrup, O. Lund
semanticscholar +1 more source
Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity
Genome Biology, 2023 Background It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome.
B. Jaegle +5 more
semanticscholar +1 more source
Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease. [PDF]
, 2017 Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle ...
Abdo, Zaid +13 more
core +5 more sources