PlainMap: a simple mapping pipeline for ancient and modern DNA

Initial public release of PlainMap, a lightweight and restartable mapping pipeline for modern and degraded DNA sequencing data.

This release includes support for heterogeneous single-end and paired-end FASTQ datasets, modern, ancient-fast, and ancient-all mapping modes, pilot subsampling, adaptive chunking, checkpoint-based restartability, fragment-aware mapping statistics, optional mapDamage analysis, and unmapped-read export.

The repository also includes a runnable example, automated regression tests, and the manifests and commands used for the manuscript evaluation.