Evaluation of CircRNA Sequence Assembly Methods Using Long Reads
Frontiers in Genetics, 2022 The functional study on circRNAs has been increasing in the past decade due to its important roles in micro RNA sponge, protein coding, the initiation, and progression of diseases.
Jingjing Zhang +8 more
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Anchorage accurately assembles anchor-flanked synthetic long reads [PDF]
Algorithms for Molecular BiologyModern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately ...
Xiaofei Carl Zang +5 more
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Detecting foldback artifacts in long-reads [PDF]
BMC GenomicsLong-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of a foldback artifact in long-read data.
Jakob M. Heinz +2 more
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Hybrid-hybrid correction of errors in long reads with HERO [PDF]
Genome Biology, 2023 Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO,
Xiongbin Kang +3 more
doaj +2 more sources
Merging short and stranded long reads improves transcript assembly. [PDF]
PLoS Computational Biology, 2023 Long-read RNA sequencing has arisen as a counterpart to short-read sequencing, with the potential to capture full-length isoforms, albeit at the cost of lower depth.
Amoldeep S Kainth +3 more
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LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads [PDF]
Genome BiologyTandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis, especially ...
Helyaneh Ziaei Jam +5 more
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Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation [PDF]
BMC BioinformaticsTelomeres are regions of repetitive DNA at the ends of linear chromosomes which protect chromosome ends from degradation. Telomere lengths have been extensively studied in the context of aging and disease, though most studies use average telomere lengths
Zachary Stephens, Jean-Pierre Kocher
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Detecting haplotype-specific transcript variation in long reads with FLAIR2 [PDF]
Genome BiologyBackground RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases.
Alison D. Tang +5 more
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
PLoS Computational Biology, 2017 The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can ...
Ryan R Wick +3 more
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CuReSim-LoRM: A Tool to Simulate Metabarcoding Long Reads [PDF]
International Journal of Molecular Sciences, 2023 Ségolène Caboche, Delphine Beury
exaly +2 more sources