seqspec is a machine-readable YAML file format for genomic library sequence and structure. It was inspired by and builds off of the Teichmann Lab Single Cell Genomics Library Structure by Xi Chen.

Genomic library structure depends on the assay used, and read structure depends additionally on the sequencer used to sequence the library. Therefore, a seqspec is specific to both a single-cell genomics assay and sequencer.

A list of seqspec examples for multiple assays and sequencers can be found in the specs/ folder. Each spec.yaml describes the 5'->3' "Final library structure" for the assay and sequencer. Sequence specification files can be formatted with the seqspec command line tool.

# development
pip install git+https://github.com/IGVF/seqspec.git

# verify install
seqspec --help

Documentation:

• docs/TUTORIAL.md : Write a seqspec
• docs/CONTRIBUTING.md : Contribute a seqspec
• docs/SPECIFICATION.md: The seqspec specification
• YouTube video that introduces seqspec
• bioRxiv preprint that describes seqspec