ArticleBioinformatics (Oxford, England)2024
A machine-readable specification for genomics assays.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Harvesting more reads from single-cell combinatorial barcoding data with scarecrow.Bioinformatics (Oxford, England) · 2026Article
- Basal cell adhesion molecule (BCAM) promotes mesothelial-to-mesenchymal transition and tumor angiogenesis through paracrine signaling.Cell communication and signaling : CCS · 2025Article
- Flexible parsing, interpretation, and editing of technical sequences with splitcode.Bioinformatics (Oxford, England) · 2024Article
- Reciprocal crosstalk between Th17 and mesothelial cells promotes metastasis-associated adhesion of ovarian cancer cells.Clinical and translational medicine · 2024Article
- Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.The Plant cell · 2024Article
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
- Flexible parsing, interpretation, and editing of technical sequences with splitcode.bioRxiv : the preprint server for biology · 2023Article
- simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry.Bioinformatics (Oxford, England) · 2023Article
- Universal preprocessing of single-cell genomics data.bioRxiv : the preprint server for biology · 2023Article
- simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry.bioRxiv : the preprint server for biology · 2023Article
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3 authors.
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Abstract
motivationUnderstanding 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.
resultsWe 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.