ArticleBioinformatics (Oxford, England)2019
Improved indel detection in DNA and RNA via realignment with ABRA2.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Metavac-RSV mucosal bivalent vaccine candidate protects cotton rats against pneumoviruses and is produced using serum-free cell culture in bioreactor.NPJ vaccines · 2025Article
- Racial differences in endometrial cancer genomics and outcomes using UNCseqGynecologic oncology reports · 2025Article
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- Clonal hematopoiesis in metastatic urothelial and renal cell carcinoma.NPJ precision oncology · 2025Article
- Application of Whole-Exome Sequencing (WES) for Prenatal Determination of Causes of Fetal Abnormalities.Genes · 2025Article
- Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors.Cancer research · 2025Article
- The mutational landscape and its longitudinal dynamics in relapsed and refractory classic Hodgkin lymphoma.Annals of hematology · 2025Article
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Corrections and comments
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3 authors.
Funding
Abstract
motivationGenomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both cancer and Mendelian disorders. Insertions and deletions (indels) are a common source of variation and can frequently impact functionality, thus making their detection vitally important. While substantial effort has gone into detecting indels from DNA, there is still opportunity for improvement. Further, detection of indels from RNA-Seq data has largely been an afterthought and offers another critical area for variant detection.
resultsWe present here ABRA2, a redesign of the original ABRA implementation that offers support for realignment of both RNA and DNA short reads. The process results in improved accuracy and scalability including support for human whole genomes. Results demonstrate substantial improvement in indel detection for a variety of data types, including those that were not previously supported by ABRA. Further, ABRA2 results in broad improvements to variant calling accuracy across a wide range of post-processing workflows including whole genomes, targeted exomes and transcriptome sequencing. AVAILABILITY AND IMPLEMENTATION: ABRA2 is implemented in a combination of Java and C/C++ and is freely available to all from: https://github.com/mozack/abra2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.