ArticleBioinformatics (Oxford, England)2020
grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research.Bioinformatics (Oxford, England) · 2026Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- A computational framework for extracting biological insights from SRA cancer data.Scientific reports · 2025Article
- GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data.Bioinformatics (Oxford, England) · 2024Article
- Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics.PeerJ · 2024Article
- Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis.Cell host & microbe · 2023Article
- Article
- Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales.Journal of virology · 2021Article
- The human virome: assembly, composition and host interactions.Nature reviews. Microbiology · 2021Review
- Rengasvirus, a Circular Replication-Associated Protein-Encoding Single-Stranded DNA Virus-Related Genome That Is a Common Contaminant in Metagenomic Data.Microbiology resource announcements · 2021Article
- DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data.Frontiers in microbiology · 2021Article
- Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease.Journal of Crohn's & colitis · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
summaryHigh-throughput sequencing is a powerful technique for addressing biological questions. Grabseqs streamlines access to publicly available metagenomic data by providing a single, easy-to-use interface to download data and metadata from multiple repositories, including the Sequence Read Archive, the Metagenomics Rapid Annotation through Subsystems Technology server and iMicrobe. Users can download data and metadata in a standardized format from any number of samples or projects from a given repository with a single grabseqs command. AVAILABILITY AND IMPLEMENTATION: Grabseqs is an open-source tool implemented in Python and licensed under the MIT license. The source code is freely available at https://github.com/louiejtaylor/grabseqs, the Python Package Index and Anaconda Cloud repository. CONTACT: bushman@pennmedicine.upenn.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.