Bamsnap-LRS: an automated batch visualization tool for long-read sequencing alignments

Abstract

SummaryLong-read sequencing (LRS) has become essential for genome assembly, structural variations (SVs) detection, haplotype phasing and transcript isoform characterization. However, these applications often require manual inspection of read alignment for validation. Existing visualization tools are either interactive genome browsers that are difficult to scale to large datasets or batch-oriented tools that are not optimized for the unique alignment patterns of long-read data. We developed Bamsnap-LRS, an automated command-line tool for high-throughput LRS alignment visualization. It supports long-read-specific features, phased SNP inspection, and publication-ready batch figure generation within a unified framework for genomic, transcriptomic, and haplotype-aware analyses. Availability and ImplementationAll codes and examples are freely available at https://github.com/comery/Bamsnap-LRS. ContactChentao Yang (yangchentao@genomics.cn) and Yang Zhou (zhouyang@genomics.cn). Supplementary informationSupplementary Table 1 and Supplementary Figures 1-8 are available at xxx online.