Dataset Information

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.

ABSTRACT: Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

SUBMITTER: Fatima N

PROVIDER: S-EPMC7760597 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.

Fatima Nazeefa N Petri Anna A Gyllensten Ulf U Feuk Lars L Ameur Adam A

Genes 20201130 12

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to ...[more]

PMID: 33266238

Similar Datasets

Project description:BackgroundStructural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The detection of structural variations in bacteria is challenging, and the recognition of even small rearrangements can be important. Even though most detection tools are aimed at and benchmarked on eukaryotic genomes, they can also be used on prokaryotic genomes. The key features of detection are the ability to detect small rearrangements and support haploid genomes. Because of the limiting performance of a single detection tool, combining the detection abilities of multiple tools can lead to more robust results. There are already available workflows for structural variation detection for long-reads technologies and for the detection of single-nucleotide variation and indels, both aimed at bacteria. Yet we are unaware of structural variations detection workflows for the short-reads sequencing platform. Motivated by this gap we created our workflow. Further, we were interested in increasing the detection performance and providing more robust results.ResultsWe developed an open-source bioinformatics pipeline, ProcaryaSV, for the detection of structural variations in bacterial isolates from paired-end short sequencing reads. Multiple tools, starting with quality control and trimming of sequencing data, alignment to the reference genome, and multiple structural variation detection tools, are integrated. All the partial results are then processed and merged with an in-house merging algorithm. Compared with a single detection approach, ProcaryaSV has improved detection performance and is a reproducible easy-to-use tool.ConclusionsThe ProcaryaSV pipeline provides an integrative approach to structural variation detection from paired-end next-generation sequencing of bacterial samples. It can be easily installed and used on Linux machines. It is publicly available on GitHub at https://github.com/robinjugas/ProcaryaSV .

Dataset Information

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.

Publications

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets