eXNVerify: coverage analysis for long and short-read sequencing data in clinical context
Porebski, S.; Stokowy, T.
Show abstract
Accurate identification of genetic variants to a large extent is based on type of experimental technology, quality of the material and coverage of obtained sequencing data. Our motivation was to create a tool that will evaluate genome coverage and accelerate the introduction of long-read sequencing to medical diagnostics and clinical practice. Here we present eXNVerify: a tool for inspection of clinical data in the context of pathogenic variants. The tool calculates Clinical Depth Coverage - a measure of coverage which we introduce to evaluate loci with pathogenic germline and somatic variants reported in ClinVar. The tool additionally provides visualization options for user-defined genes of interest. Finally, we present an examples of BRCA1, TP53, CFTR application and results of a test conducted in the Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development. eXNVerify is available at https://github.com/porebskis/eXNVerify and can be directly pulled from the DockerHub repository: docker pull porebskis/exnverify:1.0.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants. 97%
- ATAV: a comprehensive platform for population-scale genomic analyses 96%
- CNVizard: a lightweight streamlit application for an interactive analysis of copy number variants 96%
Similar papers in this journal
- MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection 96%
- unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level 95%
- BamToCov: an efficient toolkit for sequence coverage calculations 95%
Similar papers in this journal
- STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data 95%
- KATK: fast genotyping of rare variants directly from unmapped sequencing reads 93%
- Cancer SIGVAR: A semi-automated interpretation tool for germline variants of hereditary cancer-related genes 93%
Similar papers in this journal
- GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation 93%
- genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists 93%
- Accuracy and Reproducibility of Somatic Point Mutation Calling in Clinical-Type Targeted Sequencing Data 92%
Similar papers in this journal
- DivBrowse - interactive visualization and exploratory data analysis of variant call matrices 96%
- SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat 96%
- CNVpytor: a tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing 96%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.