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A machine-readable specification for genomics assays.

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.

SUBMITTER: Booeshaghi AS

PROVIDER: S-EPMC11009023 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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A machine-readable specification for genomics assays.

Booeshaghi Ali Sina AS Chen Xi X Pachter Lior L

Bioinformatics (Oxford, England) 20240301 4

<h4>Motivation</h4>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.<h4>Results</h4>We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tr ...[more]

PMID: 38579259

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