basep

BaseP is a lightweight, open-source framework for encoding and processing base-level sequence information in computational biology simulations. It defines a compact representation for nucleotide bases, base pairs, and related annotations, and provides tools to serialize data into a binary baseP file format as well as JSON metadata wrappers. The project emphasizes simplicity, portability, and extendability for research and education.

Origin and development: BaseP emerged as a community-driven project in the early 2020s to address the lack of a standardized yet flexible base-level data model for simulations. It is maintained by volunteers and hosted on public repositories. While not tied to any single organization, it aims to complement established formats such as FASTA and FASTQ by focusing on per-base annotations and pairings.

Key features: The baseP data model represents bases as elementary units with optional annotations (quality scores, confidence, modifications). It includes support for canonical and ambiguous bases, and for base-pair relations in double-stranded contexts. The library provides APIs in C, Python, and Java, along with utilities to convert to and from common formats, perform mutation simulations, and validate data integrity. It also supports streaming processing for large datasets.

Applications: BaseP is used in teaching laboratories to illustrate sequence models, in small-scale simulations of genome editing, and in research pipelines that need per-base annotations along with efficient I/O. It aims to interoperate with existing workflows through adapters and export options.

Limitations and status: BaseP is a developing project with evolving specifications; users should verify compatibility with their tools and consider contributing improvements. It remains one option among several to represent per-base data in computational workflows.