Modifying Reference Sequence and Annotation Files Quickly and Reproducibly with Ref Orm

Summary: With the increased use of genome editing tools such as CRISPR/Cas9, and the widespread use of reference genome based bioinformatic analyses, it is increasingly necessary to edit reference genome sequences and annotations to include novel sequences and features in engineered genomes (e.g. transgenes, protein fusions, and selectable markers). Whereas it is possible to manually edit sequences and annotations, the process is time-consuming and prone to error. However, failing to update reference data to match edits in corresponding genomes can result in findings that are misleading and incorrect. Here we describe ref orm, a novel tool that provides a simple, reproducible solution for creating modified reference data for use with standard bioinformatic analysis pipelines. ref orm was developed in Python3, is open-source, and freely available for download through GitHub (https://github.com/gencorefacility/reform), with detailed documentation and examples available at https://gencore.bio.nyu.edu/reform. To ensure ref orm is accessible to all users, a web-based application with a full graphical user interface has also been developed (https://reform.bio.nyu.edu).