ArticleGigaScience2022
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Pangenome-wide identification of chloroplast RNA splicing and ribosome maturation (CRM) genes in eight Pyrus genomes indicated their involvement in multiple stresses.Scientific reports · 2026Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.GigaScience · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOne of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data generated by the next-generation sequencing (NGS) technologies, this approach is often not available. The hierarchical organization of the NGS records is primarily designed for browsing or text-based searches of the information provided in metadata-related keywords, limiting the efficiency of database exploration.
findingsWe developed an automated pipeline that incorporates the well-established NGS data-processing tools and procedures to allow easy and effective sampling of the NCBI SRA database records. Given a file with query nucleotide sequences, our tool estimates the matching content of SRA accessions by probing only a user-defined fraction of a record's sequences. Based on the selected parameters, it allows performing a full mapping experiment with records that meet the required criteria. The pipeline is designed to be easy to operate-it offers a fully automatic setup procedure and is fixed on tested supporting tools. The modular design and implemented usage modes allow a user to scale up the analyses into complex computational infrastructure.
conclusionsWe present an easy-to-operate and automated tool that expands the way a user can access and explore the information contained within the records deposited in the NCBI SRA database.
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Registered trials
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.