ArticleBioinformatics (Oxford, England)2015
Starcode: sequence clustering based on all-pairs search.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 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
127 citing papers in PubMed.
- Deep mutational scanning reveals the antibody escape and infectivity landscape of SARS-CoV-2 Omicron JN.1 and XEC receptor-binding domains.Emerging microbes & infections · 2026Article
- Clonal lineage tracing and parallel multiomics profiling reveal transcriptional heterogeneity induced by ARID1A deficiency.Science advances · 2026Article
- Serum Escape Landscape of SARS-CoV-2 Omicron JN.1 and XEC RBD Under COVID-19 Vaccine Breakthrough Immunity in China.Microorganisms · 2026Article
- BCAR: a fast and indel-tolerant barcode-sequence mapper.Bioinformatics (Oxford, England) · 2026Article
- Highly efficient and low-mosaicismiScience · 2026Article
- Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.HGG advances · 2026Article
- Hierarchical lineage tracing reveals diverse pathways of cytarabine resistance.Nature communications · 2026Article
- Benchmarking DNA barcode decoding strategies under high error rates.BMC bioinformatics · 2026Article
- Multiplexed perturbation enables scalable pooled screens.Nature methods · 2026Article
- Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.Genome biology · 2026Article
- Divergent Fates of Kidney-Resident Polyomaviruses: Stable Shedding Versus Near-Silent Persistence.Viruses · 2026Article
- Comparison of state-of-the-art error-correction coding for sequence-based DNA data storage.Nature communications · 2026Article
- Divergent Fates of Kidney-Resident Polyomaviruses: Stable Shedding Versus Near-Silent Persistence.bioRxiv : the preprint server for biology · 2026Article
- Fast barcode calling based onPNAS nexus · 2026Article
- Multiplexed enrichment and tracking of lineages with CloneSweeper.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking UMI clustering tools for accurate detection of low-frequency variants from deep sequencing.Scientific reports · 2025Article
- QuiCAT: a scalable and flexible framework for mapping synthetic sequences.Bioinformatics (Oxford, England) · 2025Article
- ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples.Nucleic acids research · 2025Article
- High-throughput characterization of 5886 HER2 variants identifies 112 new in cellulo gain-of-function mutations.Genomics · 2025Article
- Protocol for multiplexed transcription factor activity detection using optimized barcoded reporters and an automated computational pipeline.STAR protocols · 2025Article
67 more citing papers are in PubMed but not listed here.
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
motivationThe increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be corrected. This is particularly important when sequencing reads from an unknown reference such as random DNA barcodes. In this case, error correction can be done by performing a pairwise comparison of all the barcodes, which is a computationally complex problem.
resultsHere, we address this challenge and describe an exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of similar sequences. The efficiency of starcode is attributable to the poucet search, a novel implementation of the Needleman-Wunsch algorithm performed on the nodes of a trie. On the task of matching random barcodes, starcode outperforms sequence clustering algorithms in both speed and precision. AVAILABILITY AND IMPLEMENTATION: The C source code is available at http://github.com/gui11aume/starcode.
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.