ArticleNature computational science2021
Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools.
Article in Nature computational science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
4 citing papers in PubMed.
- Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.NAR genomics and bioinformatics · 2026Article
- Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More).Molecular biology and evolution · 2025Article
- A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.Molecular biology and evolution · 2024Article
- Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools.Nature computational science · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
Modern DNA sequencing is used as a readout for diverse assays, with the count of aligned sequences (read depth) representing the quantitative signal for each underlying cellular phenomena. Existing data formats for quantitative genomics assays are, however, limited in either the analysis speeds they enable, the disk space they require or both. We have developed the dense depth data dump (D4) format and tool suite, with the goal of balancing improved analysis speeds with file size. The D4 format is adaptive in that it profiles a random sample of aligned sequence depth from the input sequence file to determine an optimal encoding that enables fast data access. We demonstrate that the D4 format offers substantial speed improvements over existing formats for random access, aggregation and summarization, while also achieving better or comparable file sizes. This performance enables scalable downstream analyses that would be otherwise difficult.
Identifiers
What OpenQuestion holds
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.