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