seqspec

seqspec, short for "sequence specification" (pronounced "seek-speck"), is a file format that describes data generated from genomics experiments. Both the file format and seqspec tool enable uniform processing of genomics data.

Figure 1: Anatomy of a seqspec file.

We have multiple tutorials to get you up and running with seqspec:

1. Learn how to use seqspec to standardize your genomics data preprocessing.

2. Understand how to manipulate seqspec files using the seqspec command-line tool.

Citation

The seqspec format and tool are described in this publication. If you use seqspec please cite

Ali Sina Booeshaghi, Xi Chen, Lior Pachter, A machine-readable specification for genomics assays, Bioinformatics, Volume 40, Issue 4, April 2024, btae168.

seqspec was inspired by and builds off of the Teichmann Lab Single Cell Genomics Library Structure by Xi Chen.

Documentation

• Install seqspec: docs/INSTALLATION.md
• Learn about the seqspec file format: docs/DOCUMENTATION.md
• Learn about the seqspec tool: docs/DOCUMENTATION.md
• Learn about the seqspec specification : docs/SPECIFICATION.md
• Write a seqspec: docs/TUTORIAL.md
• View example seqspec files: https://www.sina.bio/seqspec-builder/assays.html
• Contribute a seqspec : docs/CONTRIBUTING.md
• Watch a YouTube video about seqspec
• Read the manuscript that describes seqspec