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A machine-readable specification for genomics assays

Booeshaghi, A. Sina and Chen, Xi and Pachter, Lior (2023) A machine-readable specification for genomics assays. . (Unpublished)

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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. 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. The specification and associated seqspec command line tool is available at

Item Type:Report or Paper (Discussion Paper)
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URLURL TypeDescription Paper ItemIGVF / seqspec ItemSeqspec
Booeshaghi, A. Sina0000-0002-6442-4502
Chen, Xi0000-0003-2648-3146
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. We thank Delaney Sullivan for helpful discussions and Rahma Elsiesy for helpful feedback on Figure 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. A.S.B. and L.P. were supported in part by NIH 5UM1HG012077-02. The authors have declared no competing interest.
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Record Number:CaltechAUTHORS:20230322-101294000.2
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:120301
Deposited By: George Porter
Deposited On:22 Mar 2023 17:22
Last Modified:22 Mar 2023 17:22

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