Seqlengthsseqinfogr

Seqlengthsseqinfogr is a terminology used to describe a composite data artifact employed in genomic sequence analysis. It combines two linked representations: a mapping of sequence identifiers to their lengths (the seqlengths) and a graph-based depiction of sequence information (the seqinfogr).

Purpose: It provides a compact and integrated source of information useful for assembly, annotation, and graph traversal tasks, enabling efficient access to length data while exploring relationships between sequences.

Structure: The seqlengths component is typically a dictionary or table with keys as sequence IDs and values as integer lengths. The seqinfogr component is a graph where nodes represent sequences and edges indicate relationships such as overlaps, contiguity, or alignment-based connections. Node or edge attributes may store GC content, coverage, quality, or metadata.

Creation and workflow: The artifact is generated from raw sequencing outputs or assembly graphs. Lengths may be derived from sequence records in FASTA/FASTQ, while the graph is built from overlap layouts, assembly graphs, or alignment results. The combined format supports convenient data exchange between tools.

Applications and limitations: It supports fast lookups of lengths during graph traversals, visualization, and filtering. It is not a standardized format; compatibility relies on agreed serialization (JSON, YAML, or GraphML) and may be interoperable with formats such as FASTA, GFA, or igraph objects.

See also: Graph, Sequence length, Genome assembly, GFA, igraph, Bioconductor.