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NanoVar

NanoVar is a structural variant (SV) caller that uses low-depth long-read sequencing such as Oxford Nanopore Technologies (ONT ). It performs both long-read mapping (minimap2) and SV discovery in a single pipeline. NanoVar can produce rapid and accurate results by employing shallow (4x depth - homozygous SVs, 8x depth - heterozygous SVs) whole genome long-read sequencing data, which saves time and sequencing cost, especially for large-scale cohort SV-association studies or clinical SV investigations. NanoVar is able to characterize the main SV classes (Novel-insertion, transposition, translocation, deletion, inversion and tandem duplication) which are detected through split-read read analysis. It utilizes a neural-network -based algorithm to evaluate the confidence of each SV breakend based on features of true SV characteristics in simulations, thereby producing reliable SV output.

Publication

Tham, CY., Tirado-Magallanes, R., Goh, Y. et al. NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing. Genome Biol 21, 56 (2020). https://doi.org/10.1186/s13059-020-01968-7

Contents

1. Home
2. Inputs and parameters
3. Model training
4. NanoVar report
5. Output