Functional meta-omics provide critical insights into long- and short-read assemblies.
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab330
Abstract: Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity.… read more here.
Keywords: short read; functional meta; omics provide; read ... See more keywords
T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz727
Abstract: Abstract Motivation Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. Accurate genotyping of… read more here.
Keywords: short read; sequencing data; read; genome ... See more keywords
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
Sign Up to like & getrecommendations! Published in 2022 at "Microbial Genomics"
DOI: 10.1101/2022.04.29.490057
Abstract: Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only possible with hybrid assembly, combining long- (typically using nanopore sequencing) and short-read (Illumina) datasets. Being able to utilise… read more here.
Keywords: cost; bacterial genomes; r10 kit12; reconstruction ... See more keywords
A 10 MHz Read-Out Chain for Electrical Impedance Tomography
Sign Up to like & getrecommendations! Published in 2018 at "IEEE Transactions on Biomedical Circuits and Systems"
DOI: 10.1109/tbcas.2017.2778288
Abstract: This paper presents the design and implementation of a read-out chain for electrical impedance tomography (EIT) imaging. The EIT imaging approach can be incorporated to take spectral images of the tissue under study, offering an… read more here.
Keywords: impedance tomography; read; read chain; electrical impedance ... See more keywords
Long-Read- and Short-Read-Based Whole-Genome Sequencing Reveals the Antibiotic Resistance Pattern of Helicobacter pylori
Sign Up to like & getrecommendations! Published in 2023 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.04522-22
Abstract: Helicobacter pylori resistance has been increasing in recent years. The resistance profile, which is important for empirical treatment, is region and population specific. ABSTRACT The rates of antibiotic resistance of Helicobacter pylori are increasing, and… read more here.
Keywords: short read; antibiotic resistance; resistance; read ... See more keywords
A sensitive short read homology search tool for paired-end read sequencing data
Sign Up to like & getrecommendations! Published in 2017 at "BMC Bioinformatics"
DOI: 10.1186/s12859-017-1826-2
Abstract: BackgroundHomology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the… read more here.
Keywords: read; search; short pair; homology search ... See more keywords
‘Read–through marking’ reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP
Sign Up to like & getrecommendations! Published in 2018 at "Wellcome Open Research"
DOI: 10.12688/wellcomeopenres.14663.1
Abstract: We established a modified iCLIP protocol, called ‘read-through marking’, which facilitates the detection of cDNAs that have not been truncated upon encountering the RNA–peptide complex during reverse transcription (read-through cDNAs). A large proportion of these… read more here.
Keywords: reveals differential; read cdnas; read; read marking ... See more keywords
Isoform Age - Splice Isoform Profiling Using Long-Read Technologies
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2021.711733
Abstract: Alternative splicing (AS) of RNA is a key mechanism that results in the expression of multiple transcript isoforms from single genes and leads to an increase in the complexity of both the transcriptome and proteome.… read more here.
Keywords: age splice; splice isoform; read; long read ... See more keywords
Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Plant Science"
DOI: 10.3389/fpls.2021.657240
Abstract: Aligning short-read sequences is the foundational step to most genomic and transcriptomic analyses, but not all tools perform equally, and choosing among the growing body of available tools can be daunting. Here, in order to… read more here.
Keywords: short read; read; comparison short; read sequence ... See more keywords
Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Veterinary Science"
DOI: 10.3389/fvets.2022.1073919
Abstract: Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non-targeted sequencing approach with… read more here.
Keywords: short read; random sequencing; detection; read ... See more keywords