nucleofile

Nucleofile is a hypothetical, open file format designed to store nucleic acid sequences and their annotations within a single container. It aims to streamline data exchange among sequencing centers, researchers, and software tools by embedding sequence data, quality metrics, and provenance alongside descriptive metadata.

The format consists of a header with metadata such as format version, genome assembly reference, creation date, and authors, followed by a body that contains one or more sequences. Each sequence has an identifier, the nucleotide sequence, and optional per-base quality scores. Annotations—genes, features, motifs—are stored in a structured section and linked to sequence regions. Nucleofile supports extensible metadata, controlled vocabularies, external references, and both compression and indexing for fast random access.

Designed for interoperability, Nucleofile can be translated to existing formats through adapters or converters. It is envisaged for use in complete-genome archives, data sharing among laboratories, and reproducible analysis pipelines. Proponents emphasize reduced fragmentation, better traceability, and easier long-term preservation, while noting the need for broad tooling and community governance.

As a concept under discussion, Nucleofile has seen pilot implementations and reference tooling in academic demonstrations but has not achieved formal standardization. Its status is exploratory, and practical adoption would depend on consensus, tooling, and community support.

See also: FASTA, FASTQ, BAM, VCF, JSON, YAML, compression formats.