Fu-Yilei

Guide a user end-to-end through running the TBAS (Trio-Barcoded ONT Adaptive Sampling) long-read pipeline in this repository: checking the software environment, building the sample manifest, choosing which stages to run, doing a dry run, executing, and interpreting the outputs (small variants, structural variants, tandem repeats including pathogenic repeat expansions, and methylation). Use this skill whenever someone wants to run TBAS, analyze an ONT/nanopore adaptive-sampling trio, process a `calls*.bam`, call variants/SVs/tandem-repeats/methylation from long reads with this tool, or asks "how do I run this pipeline" while in the TBAS_pipeline repo — even if they don't name the stages explicitly. Assume the person may be a clinician rather than a bioinformatician and may need plain-language guidance.