ArticleGigaScience2017
Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.
Article in GigaScience, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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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.
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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
12 citing papers in PubMed.
- Reciprocal Genome Projection Reveals Reference-Conditioned Functional Variation in ClinicalPathogens (Basel, Switzerland) · 2026Article
- Detecting poliovirus sequences in the sequence read archive database using bioinformatics tools.Frontiers in bioinformatics · 2026Article
- Seasonal Changes Drive Shifts in Bacterial Community Structure and Functional Composition in the Yellow River (Zhengzhou Section).Current microbiology · 2025Article
- Secondhand Smoke Exposure Timing Triggers Distinct Placental Responses in Mouse Pregnancy.Cells · 2025Article
- Significance of KLK7 expression, polymorphisms, and function in sheep horn growth.BMC genomics · 2025Article
- NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency.Scientific data · 2023Article
- Article
- Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2021Article
- All of gene expression (AOE): An integrated index for public gene expression databases.PloS one · 2020Article
- VARUS: sampling complementary RNA reads from the sequence read archive.BMC bioinformatics · 2019Article
- Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection.GigaScience · 2019Article
- Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.GigaScience · 2017Article
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
No grant is acknowledged in the PubMed record.
Abstract
It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party.
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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.