ArticleGenome medicine2015
ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.
Article in Genome medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology.Current issues in molecular biology · 2024Review
- SpecHLA enables full-resolution HLA typing from sequencing data.Cell reports methods · 2023Article
- Article
- High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B.Histopathology · 2023Article
- Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen.PLoS genetics · 2021Article
- Correlation between dynamic susceptibility contrast perfusion MRI and genomic alterations in glioblastoma.Neuroradiology · 2021Article
- Clinical and technical assessment of MedExome vs. NGS panels in patients with suspected genetic disorders in Southwestern Ontario.Journal of human genetics · 2021Article
- Assessing acquired resistance to IDH1 inhibitor therapy by full-exonCold Spring Harbor molecular case studies · 2021Article
- Article
- Neonatal respiratory failure due to novel compound heterozygous mutations in the ABCA3 lipid transporter.Cold Spring Harbor molecular case studies · 2020Article
- Analyses of molecular and histopathologic features and expression of PRAME by immunohistochemistry in mucosal melanomas.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2019Article
- An Accurate and Comprehensive Clinical Sequencing Assay for Cancer Targeted and Immunotherapies.The oncologist · 2019Article
- NGSEP3: accurate variant calling across species and sequencing protocols.Bioinformatics (Oxford, England) · 2019Article
- Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory.Molecular genetics and metabolism reports · 2019Article
- Structural variants in 3000 rice genomes.Genome research · 2019Article
- Optimization of a microfluidics-based next generation sequencing assay for clinical oncology diagnostics.Annals of translational medicine · 2018Article
- Indel detection from DNA and RNA sequencing data with transIndel.BMC genomics · 2018Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.