Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies.
Sign Up to like & getrecommendations! Published in 2023 at "Molecular genetics & genomic medicine"
DOI: 10.1002/mgg3.2164
Abstract: BACKGROUND The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed… read more here.
Keywords: short read; characterisation; targeted nanopore; read sequencing ... See more keywords
Development and evaluation of a rapid and cost-efficient NGS-based MHC class I genotyping method for macaques by using a prevalent short-read sequencer.
Sign Up to like & getrecommendations! Published in 2021 at "Immunogenetics"
DOI: 10.1007/s00251-020-01199-x
Abstract: Rhesus macaque is one of the most widely used primate model animals for immunological research of infectious diseases including human immunodeficiency virus (HIV) infection. It is well known that major histocompatibility complex (MHC) class I… read more here.
Keywords: short read; method; ngs based; genotyping method ... See more keywords
Data mining for discovery of endophytic and epiphytic fungal diversity in short-read genomic data from deciduous trees
Sign Up to like & getrecommendations! Published in 2018 at "Fungal Ecology"
DOI: 10.1016/j.funeco.2018.04.004
Abstract: Abstract High-throughput sequencing of DNA barcodes, such as the internal transcribed spacer (ITS) of the 16s rRNA sequence, has expanded the ability of researchers to investigate the endophytic fungal communities of living plants. With a… read more here.
Keywords: short read; data mining; endophytic epiphytic; mining discovery ... See more keywords
Potential in vivo transfer of a blaCTX-M14-harbouring plasmid established by combining long- and short-read sequencing.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of microbiological methods"
DOI: 10.1016/j.mimet.2019.02.004
Abstract: Horizontal transfer of plasmid-mediated antibiotic resistance has rarely been documented in vivo. Utilizing long-read (Oxford Nanopore) and short-read (Illumina) sequencing, we confirmed that a gut-colonizing Escherichia coli and a hypervirulent Klebsiella pneumoniae ST23, isolated from… read more here.
Keywords: short read; blactx; potential vivo; transfer ... See more keywords
Whisper 2: Indel-sensitive short read mapping
Sign Up to like & getrecommendations! Published in 2021 at "SoftwareX"
DOI: 10.1016/j.softx.2021.100692
Abstract: Abstract Identification of genetic variants is of crucial importance in the forthcoming era of precision medicine. Since the majority of variant callers require mapping reads to a reference genome, the reliability of the latter is… read more here.
Keywords: whisper indel; read mapping; short read; indel sensitive ... See more keywords
Comparison of mitochondrial DNA variants detection using short- and long-read sequencing
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Human Genetics"
DOI: 10.1038/s10038-019-0654-9
Abstract: The recent advent of long-read sequencing technologies is expected to provide reasonable answers to genetic challenges unresolvable by short-read sequencing, primarily the inability to accurately study structural variations, copy number variations, and homologous repeats in… read more here.
Keywords: short read; long read; dna variants; mitochondrial dna ... See more keywords
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Sign Up to like & getrecommendations! Published in 2017 at "Nature Communications"
DOI: 10.1038/s41467-017-01343-4
Abstract: Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION… read more here.
Keywords: short read; variation; patient genomes; structural variants ... See more keywords
MetaGeneHunt for protein domain annotation in short-read metagenomes
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-63775-1
Abstract: The annotation of short-reads metagenomes is an essential process to understand the functional potential of sequenced microbial communities. Annotation techniques based solely on the identification of local matches tend to confound local sequence similarity and… read more here.
Keywords: protein; metagenehunt; short read; annotation ... See more keywords
Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and better de novo assemblies.
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in functional genomics"
DOI: 10.1093/bfgp/elac016
Abstract: Next-Generation Sequencing has produced incredible amounts of short-reads sequence data for de novo genome assembly over the last decades. For efficient transmission of these huge datasets, high-performance compression algorithms have been intensively studied. As both… read more here.
Keywords: short read; error correction; error; read sets ... See more keywords
Detection of somatic structural variants from short-read next-generation sequencing data
Sign Up to like & getrecommendations! Published in 2020 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbaa056
Abstract: Abstract Somatic structural variants (SVs), which are variants that typically impact >50 nucleotides, play a significant role in cancer development and evolution but are notoriously more difficult to detect than small variants from short-read next-generation… read more here.
Keywords: short read; detection; read next; structural variants ... See more keywords
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