Project description:Modest target sequencing yield improvements using Nanopore adaptive sampling to reduce human DNA contamination from clinical tissue samples

| PRJEB78709 | ENA

SARS-CoV-2

Project description:Nanopore adaptive sampling with carrier DNA (NASCarD)

| PRJNA930601 | ENA

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Project description:Oxford Nanopore sequence data from adaptive sampling experiments using a synthetic bacterial mock community.

| PRJEB44844 | ENA

Adaptive sampling and chromosome sorting Y chromosome data

Project description:Y chromosome chromosome sorting and adaptive sampling data

| PRJEB58141 | ENA

CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ONT adaptive sampling]

Project description:CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ONT adaptive sampling]

| PRJNA1043620 | ENA

Carrier Subclass

Project description:Carrier Subclass

| PRJNA1031099 | ENA

Nanopore adaptive sampling effectively enriches bacterial plasmids.

Project description:Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions.ImportanceAntimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an in silico method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.

| S-EPMC10949517 | biostudies-literature

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