CapScreen

CapScreen v1.0.0 First stable release of CapScreen, a pipeline for high-throughput analysis of amplicon sequencing (NGS) from AAV (Adeno-Associated Virus) library screens. What is CapScreen? CapScreen streamlines the analysis of amplicon sequencing data from AAV library screens (binding or transduction). It runs quality control, alignment, variant extraction and counting, and optional statistical analysis—from raw FASTQ files to count matrices and publication-ready plots. Highlights End-to-end pipeline: FASTQ → QC (FASTP) → read merging (PEAR) → alignment (Bowtie2) → variant counting → optional DESeq2 and statistical analysis Single-sample and batch mode: Process many samples via a CSV sample sheet Configurable: One JSON config for pipeline and analysis parameters Dockerized: Reproducible runs via the provided Docker image Reporting: HTML reports with QC metrics and interactive count tables Getting started Install: Build the Docker image: docker build -f docker/DockerFile -t capscreen . Run: See README for single-sample and batch commands. License: MIT Citation Citation information will be added after the repository is linked to Zenodo. If you use CapScreen in your work, please credit the software and cite the repository or DOI once available. Full changelog: CHANGELOG.md