Dataset for "NanoVar: a Comprehensive Workflow for Structural Variant Detection to uncover the Genome's Hidden Patterns"

Output Files for Long-Read Structural Variant and Repeat Analysis in Colorectal Cancer Samples (HRR698464, HRR698460, C586, C588) Description: This Zenodo dataset includes comprehensive output files generated during the application of a long-read sequencing analysis protocol for structural variant (SV) detection and repeat element characterization in colorectal cancer samples. The dataset is organized into two main directories: 1. HRR698464_MSI-H_TumorThis directory contains all primary output files generated from the analysis pipeline applied to the MSI-H tumor sample HRR698464 (also referred to as patient C586.T). Each subdirectory corresponds to a specific stage in the protocol: NanoPlot_outputOutput from Stage 1 – Quality assessment of raw reads using NanoPlot. SAMtools_outputBAM file processing outputs from Stage 2 – Alignment of long reads to the reference genome using SAMtools. NanoVar_outputOutput from Stage 3 – Structural variant calling using NanoVar. VCF_filtering_outputOutput from Stage 4 – Filtering of structural variants using SURVIVOR and BCFtools; includes the filtered VCF files. NanoINSight_outputOutput from Stage 5 – Characterization of repeat elements using NanoINSight. VEP_outputOutput from Stage 6 – Annotation of structural variants using Ensembl Variant Effect Predictor (VEP). 2. Additional_output_filesThis directory contains supplementary output files used for comparison and visualization in Figures 4–7 of the associated publication. These include: HRR698460.NanoPlot.report.htmlNanoPlot quality summary of a lower-quality tumor sample (HRR698460), used in Figure 4 for comparison with HRR698464. C586.N.nanovar.pass.vcfNanoVar VCF output for the matched normal sample of patient C586, used to filter somatic calls in Stage 4. C586.N.nanovar.pass.report.htmlNanoVar summary report of the normal sample of C586; used in Figure 5a. C588.N.nanovar.pass.vcfNanoVar VCF output of the MSS normal sample (C588) for comparison with the MSI-H patient (C586). C588.N.nanovar.pass.report.htmlNanoVar summary report of the MSS normal sample; used in Figure 5b. C588.T.nanovar.pass.vcfNanoVar VCF output of the MSS tumor sample (C588); used in comparative analyses with the MSI-H sample. C588.T.nanovar.pass.report.htmlNanoVar summary report of the MSS tumor sample; used in Figure 5b. MSS.tumor.unique.vcfVCF file of somatic SVs in the MSS sample, generated by comparing matched tumor and normal pairs. MSS.tumor.unique.RepeatMasker.tblRepeatMasker output annotating somatic insertions in the MSS tumor sample; used in Figure 6. MSS.tumor.unique.vep.htmlEnsembl VEP annotation report of somatic SVs in the MSS patient; used in Figures 7a and 7b. This dataset supports reproducibility and transparency of the protocol and offers a valuable resource for researchers interested in long-read-based SV detection, repeat annotation, and comparative cancer genomics.