OBLX: building standardized reference resources for reproducible bioinformatics data analysis

Reproducible next-generation sequencing (NGS) analyses in cancer research require standardized reference genome resources, yet these resources are often assembled inconsistently, limiting the comparability of results across pipelines and studies. While existing solutions support a range of workflows, they provide only limited documentation of the included data and processing steps. Furthermore, some of these resources are not version-matched or outdated, making them less suitable for integrated and reproducible cancer genomics analyses. To address this gap, we developed the Omics builder for Bioinformatics resource Libraries and indeXes (OBLX, https://github.com/TRON-Bioinformatics/oblx/), a fully documented, configurable and reproducible pipeline for building standardized NGS reference libraries. First, the pipeline retrieves genome and transcriptome reference sequences, their corresponding annotations, and population variant resources from public sources. Subsequently, OBLX processes these resources to ensure compatibility with commonly used NGS tools, which includes building several bioinformatic indices. The resulting OBLX library may then be directly used by downstream tools and pipelines. By documenting all resources, operations, and intended use-cases, OBLX improves transparency, reproducibility, and interoperability for NGS data analyses.