Results 11 to 20 of about 327,413 (252)
Resolving repeat families with long reads [PDF]
BMC Bioinformatics, 2019 Draft quality genomes for a multitude of organisms have become common due to the advancement of genome assemblers using long-read technologies with high error rates. Although current assemblies are substantially more contiguous than assemblies based on short reads, complete chromosomal assemblies are still challenging. Interspersed repeat families with
Philipp Bongartz
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Anchorage accurately assembles anchor-flanked synthetic long reads. [PDF]
Algorithms Mol BiolModern 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 ...
Zang XC +5 more
europepmc +3 more sources
Hybrid-hybrid correction of errors in long reads with HERO. [PDF]
Genome Biol, 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,
Kang X, Xu J, Luo X, Schönhuth A.
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Chloroplast genome draft assembly of Falcataria moluccana using hybrid sequencing technology
BMC Research Notes, 2023 Objectives Falcataria moluccana, known locally as Sengon, is a fast-growing legume tree that is commonly planted in community forests of Java Island, Indonesia. However, the plantations face attacks of Boktor stem borer (Xystrocera festiva) and gall-rust
Vilda Puji Dini Anita +2 more
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Short paired-end reads trump long single-end reads for expression analysis
BMC Bioinformatics, 2020 Background Typical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired ...
Adam H. Freedman +2 more
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Merging short and stranded long reads improves transcript assembly. [PDF]
PLoS Comput Biol, 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.
Kainth AS +3 more
europepmc +2 more sources
A comprehensive investigation of metagenome assembly by linked-read sequencing
Microbiome, 2020 Background The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities.
Lu Zhang +8 more
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LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads. [PDF]
Genome BiolTandem 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 ...
Ziaei Jam H +5 more
europepmc +2 more sources
Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing. [PDF]
PLoS ONE, 2016 Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences.
James A Stapleton +12 more
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Comparison and benchmark of structural variants detected from long read and long-read assembly
Briefings in Bioinformatics, 2023 Abstract Structural variant (SV) detection is essential for genomic studies, and long-read sequencing technologies have advanced our capacity to detect SVs directly from read or de novo assembly, also known as read-based and assembly-based strategy. However, to date, no independent studies have compared and benchmarked the two strategies.
Jiadong Lin +4 more
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