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Published April 2024 | Published
Journal Article Open

A machine-readable specification for genomics assays

Booeshaghi, Ali Sina ORCID icon
Chen, Xi ORCID icon
Pachter, Lior1 ORCID icon
  • 1. ROR icon California Institute of Technology

Abstract

Motivation

Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libraries.

Results

We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tracking and comparison of genomics assays.

Availability and implementation

The specification and associated seqspec command line tool is available at https://www.doi.org/10.5281/zenodo.10213865.

Copyright and License

© The Author(s) 2024. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Acknowledgement

We thank Delaney Sullivan for helpful discussions and Rahma Elsiesy for helpful feedback on Fig. 1. Discussions with the Impact of Genomics Variation on Function (IGVF) Single-Cell Focus Group helped to shape some features of seqspec. Thanks to Idan Gabdank for useful feedback on seqspec and for suggesting the md5 checksum. Meichen Fang contributed the sci-RNA-seq3 seqspec. This work was primarily undertaken while A.S.B. was at the California Institute of Technology.

Funding

This work was supported in part by NIH [5UM1HG012077-02 to A.S.B. and L.P.]. The authors also acknowledge the Howard Hughes Medical Institute for funding A.S.B. through the Hanna H. Gray Fellows program.

Data Availability

The specification and associated seqspec command line tool is available at https://www.doi.org/10.5281/zenodo.10213865 as well as on GitHub https://github.com/pachterlab/seqspec.

Supplementary data are available at Bioinformatics online.

Conflict of Interest

None declared.

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Additional details

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April 15, 2024
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