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:
-
Learn how to use
seqspecto standardize your genomics data preprocessing. -
Understand how to manipulate
seqspecfiles using theseqspeccommand-line tool.
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.
- Install
seqspec:docs/INSTALLATION.md - Learn about the
seqspecfile format:docs/DOCUMENTATION.md - Learn about the
seqspectool:docs/DOCUMENTATION.md - Learn about the
seqspecspecification :docs/SPECIFICATION.md - Write a
seqspec:docs/TUTORIAL.md - View example
seqspecfiles: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