[q-bio.GN] Mapping sequencing reads to a reference genome requires preprocessing and alignment choices that can vary with library type, fragment length, sequencing platform, and reference genome.
![Overview of the PlainMap mapping workflow. PlainMap processes heterogeneous FASTQ input through header-based pairing inference, pilot subsampling and deterministic chunking, fastp preprocessing, mode-specific mapping, BAM processing, and summary-statistic generation. Optional outputs include mapDamage analyses and FASTQ files containing unmapped reads. -- [q-bio.GN]](https://i0.wp.com/astrobiology.com/wp-content/uploads/2026/09/PlainMap.png?resize=1200%2C719&ssl=1)
[q-bio.GN] Mapping sequencing reads to a reference genome requires preprocessing and alignment choices that can vary with library type, fragment length, sequencing platform, and reference genome.