ArticleBioinformatics (Oxford, England)2020
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets.
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 29 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
29 citing papers in PubMed, 71 citations in OpenAlex.
- Article
- BiTUGA: scalable prevalence-based unitig association testing for binary traits.G3 (Bethesda, Md.) · 2026Article
- CircZBTB46, a promising therapeutic target in crizotinib resistant ALK-positive T lymphomas.Leukemia · 2026Article
- CircRNAs derived from the tyrosine phosphatase PTPN22 impact chemosensitivity in ALK-positive T-cell lymphomas.Scientific reports · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Acute myeloid leukemia risk stratification in younger and older patients through transcriptomic machine learning models.Scientific reports · 2025Article
- MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.Bioinformatics (Oxford, England) · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data.Genome biology · 2024Article
- Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq.NAR genomics and bioinformatics · 2024Article
- Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets.Bioinformatics (Oxford, England) · 2024Article
- Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.Bioinformatics (Oxford, England) · 2024Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Compression Algorithm for Colored de Bruijn Graphs.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
- On weighted k-mer dictionaries.Algorithms for molecular biology : AMB · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants.Bioinformatics (Oxford, England) · 2023Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationIn this work we present REINDEER, a novel computational method that performs indexing of sequences and records their abundances across a collection of datasets. To the best of our knowledge, other indexing methods have so far been unable to record abundances efficiently across large datasets.
resultsWe used REINDEER to index the abundances of sequences within 2585 human RNA-seq experiments in 45 h using only 56 GB of RAM. This makes REINDEER the first method able to record abundances at the scale of ∼4 billion distinct k-mers across 2585 datasets. REINDEER also supports exact presence/absence queries of k-mers. Briefly, REINDEER constructs the compacted de Bruijn graph of each dataset, then conceptually merges those de Bruijn graphs into a single global one. Then, REINDEER constructs and indexes monotigs, which in a nutshell are groups of k-mers of similar abundances. AVAILABILITY AND IMPLEMENTATION: https://github.com/kamimrcht/REINDEER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
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.