ArticleGenes & genomics2018
Performance evaluation method for read mapping tool in clinical panel sequencing.
Article in Genes & genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Prediction of antimicrobial resistance inMicrobiology spectrum · 2025Article
- Comparative analysis of batch correction methods for FDG PET/CT using metabolic radiogenomic data of lung cancer patients.Scientific reports · 2023Article
- Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.PloS one · 2023Article
- A Protocol for Genome-Wide Analysis of DNA Replication Timing in Intact Root Tips.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions.Genome medicine · 2021Article
- Genome assembly using quantum and quantum-inspired annealing.Scientific reports · 2021Article
- Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels.BMC bioinformatics · 2021Article
- Parallel comparison and combining effect of radiomic and emerging genomic data for prognostic stratification of non-small cell lung carcinoma patients.Thoracic cancer · 2020Article
- Metabolic radiogenomics in lung cancer: associations between FDG PET image features and oncogenic signaling pathway alterations.Scientific reports · 2020Article
- Clinical Targeted Next-Generation sequencing Panels for Detection of Somatic Variants in Gliomas.Cancer research and treatment · 2020Article
- RNA-Seq profiling of circular RNAs and potential function of hsa_circ_0002360 in human lung adenocarcinom.American journal of translational research · 2019Article
- Selection of Optimal Bioinformatic Tools and Proper Reference for Reducing the Alignment Error in Targeted Sequencing Data.Journal of medical signals and sensorsArticle
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In addition to the rapid advancement in Next-Generation Sequencing (NGS) technology, clinical panel sequencing is being used increasingly in clinical studies and tests. However, tools that are used in NGS data analysis have not been comparatively evaluated in performance for panel sequencing. This study aimed to evaluate the tools used in the alignment process, the first procedure in bioinformatics analysis, by comparing tools that have been widely used with ones that have been introduced recently. With the accumulated panel sequencing data, detected variant lists were cataloged and inserted into simulated reads produced from the reference genome (h19). The amount of unmapped reads and misaligned reads, mapping quality distribution, and runtime were measured as standards for comparison. As the most widely used tools, Bowtie2 and BWA-MEM each showed explicit performance with AUC of 0.9984 and 0.9970 respectively. Kart, maintaining superior runtime and less number of misaligned read, also similarly possessed high level of AUC (0.9723). Such selection and optimization method of tools appropriate for panel sequencing can be utilized for fields requiring error minimization, such as clinical application and liquid biopsy studies.
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