Decoupling alignment strategy from feature quantification using a standard alignment incidence data structure

Summary The abundance of genomic feature such as gene expression is often estimated from observed total number of alignment incidences in the targeted genome regions. We introduce a generic data structure and associated file format for alignment incidence data so that method developers can create novel pipelines comprising models, each optimal for read alignment, post-alignment QC, and quantification across multiple sequencing modalities. Availability and Implementation alntools software is freely available at under MIT license. Contact kb.choi{at}jax.org or gary.churchill{at}jax.org ### Competing Interest Statement The authors have declared no competing interest.