DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data

Marriott, Heather; Kabiljo, Renata; Khleifat, Ahmad Al; Dobson, Richard; Al‐Chalabi, Ammar; Iacoangeli, Alfredo

doi:10.1093/bioinformatics/btad152

Cited by 4 publications

(1 citation statement)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The interactive PDF report and cBioPortal facilitate discussion and decision-making processes by presenting data in a clear and concise manner. Other existing pipelines, e.g., [ 63 , 64 , 65 , 66 ], do not yet provide a comparatively in-depth and clearly structured presentation of genetic variants, quality metrics, complex biomarkers, CNVs, and RNA fusions in single outputs.…”

Section: Discussionmentioning

confidence: 99%

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

Metzger

Hess

Blaumeiser

et al. 2023

Cancers

View full text Add to dashboard Cite

(1) Background: Next-generation sequencing (NGS) of patients with advanced tumors is becoming an established method in Molecular Tumor Boards. However, somatic variant detection, interpretation, and report generation, require in-depth knowledge of both bioinformatics and oncology. (2) Methods: MIRACUM-Pipe combines many individual tools into a seamless workflow for comprehensive analyses and annotation of NGS data including quality control, alignment, variant calling, copy number variation estimation, evaluation of complex biomarkers, and RNA fusion detection. (3) Results: MIRACUM-Pipe offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (4) Conclusions: MIRACUM-Pipe, a versatile pipeline for NGS, can be customized according to bioinformatics and clinical needs and to support clinical decision-making with visual processing and interactive reporting.

show abstract

Section: Discussionmentioning

confidence: 99%

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

Metzger

Hess

Blaumeiser

et al. 2023

Cancers

View full text Add to dashboard Cite

show abstract

Next generation sequencing-based transcriptome data mining for virus identification and characterization: Review on recent progress and prospects

Rahimian,

Panahi

2024

Journal of Clinical Virology Plus

View full text Add to dashboard Cite

Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing

Santos,

Lee,

Williams

et al. 2024

Preprint

View full text Add to dashboard Cite

Oxford Nanopore Technologies (ONT) long-read sequencing (LRS) has emerged as a promising tool for genomic analysis, but comprehensive comparisons with established platforms across diverse datasets remain limited. In this study, we present a comprehensive comparison of ONT long-read sequencing (LRS) against Illumina short- read sequencing (SRS) and microarray platforms across 14 human genomes.We performed ONT sequencing using both multiplexed and singleplexed approaches and compared the results with matched Illumina microarray and SRS data. We assessed sequencing quality metrics, variant detection performance for single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants (SVs), while examining the impact of sequencing depth, read length, and multiplexing.ONT LRS demonstrated competitive performance with SRS for SNV detection, particularly in low complexity regions (F-measure: 0.763 vs 0.770), though with slightly lower performance in high complexity regions (F-measure: 0.954 vs 0.968). For indel detection, LRS showed robust performance in high complexity regions (F-measure: 0.850) which, however, decreased in low complexity regions (F-measure: 0.453). LRS identified 2.82 times more structural variants than SRS and detected variants across a broader size range (8 bp to 129 Mb vs 2 bp to 6 kb). Sequencing depth strongly correlated with variant calling performance across all variant types, with correlation coefficients of 0.80 for SNVs in high complexity regions, 0.84 for SNVs in low complexity regions, and exceeding 0.9 for indels. SV detection in LRS showed strong depth dependence (r = 0.939), while SRS SV calls remained stable across depths.Our findings demonstrate that ONT LRS complements existing sequencing technologies, offering advantages in detecting structural variants and analysing low complexity regions, while maintaining competitive performance in standard variant detection. This study provides practical insights for optimising ONT sequencing strategies and highlights areas for future methodological improvement.

show abstract

DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data

Cited by 4 publications

References 18 publications

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

Next generation sequencing-based transcriptome data mining for virus identification and characterization: Review on recent progress and prospects

Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing

Contact Info

Product

Resources

About