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. 2024 Mar 29;40(4):btae168.
doi: 10.1093/bioinformatics/btae168.

A machine-readable specification for genomics assays

Ali Sina Booeshaghi  1 , Xi Chen  2 , Lior Pachter  3   4
Affiliations

A machine-readable specification for genomics assays

Ali Sina Booeshaghi et al. Bioinformatics. .

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.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
The structure of molecules in genomic libraries. Sequencing libraries are constructed by combining Atomic Regions to form an adapter-insert-adapter construct. The seqspec for the assay annotates the construct with Regions and meta Regions.
Figure 2.
Figure 2.
Uniform processing enabled with seqspec. The seqspec index command produces a technology string that identifies appropriate sequence elements and can be passed into processing tools.
See this image and copyright information in PMC

Update of

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