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Project description
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
:
-
Learn how to use
seqspec
to standardize your genomics data preprocessing. -
Understand how to manipulate
seqspec
files using theseqspec
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
Project details
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