ArticleBioinformatics (Oxford, England)2014
BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 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
46 citing papers in PubMed.
- A Pangenome Framework Reveals Conserved Pathogenicity-Associated Biosynthetic Gene Clusters in Fusarium equiseti, a Root Rot Pathogen of Panax notoginseng.Molecular plant pathology · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Ghosts of symbionts past: the hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts.G3 (Bethesda, Md.) · 2025Article
- Comparative Genomic Analysis of Co-Occurring Hybrid Zones of House Mouse Parasites Pneumocystis murina and Syphacia obvelata Using Genome Polarisation.Molecular ecology · 2025Article
- How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.Quantitative biology (Beijing, China) · 2025Review
- Chromosome-level genome assembly and annotation of pawak croaker (Pennahia pawak).Scientific data · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Illumina reads correction: evaluation and improvements.Scientific reports · 2024Article
- Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing.BMC bioinformatics · 2022Article
- K-Mer Spectrum-Based Error Correction Algorithm for Next-Generation Sequencing Data.Computational intelligence and neuroscience · 2022Article
- Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach.Nucleic acids research · 2021Article
- Feather Gene Expression Elucidates the Developmental Basis of Plumage Iridescence in African Starlings.The Journal of heredity · 2021Article
- Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production.Microorganisms · 2021Review
- Benchmarking of computational error-correction methods for next-generation sequencing data.Genome biology · 2020Article
- Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild.Evolution letters · 2020Article
- The genome of the butternut canker pathogen,PeerJ · 2020Article
- When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data.Genome biology · 2019Review
- Illumina error correction near highly repetitive DNA regions improves de novo genome assembly.BMC bioinformatics · 2019Article
- Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters.BioMed research international · 2019Article
- Genomic signatures of local adaptation to the degree of environmental predictability in rotifers.Scientific reports · 2018Article
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.
Funding
Abstract
motivationRapid advances in next-generation sequencing (NGS) technology have led to exponential increase in the amount of genomic information. However, NGS reads contain far more errors than data from traditional sequencing methods, and downstream genomic analysis results can be improved by correcting the errors. Unfortunately, all the previous error correction methods required a large amount of memory, making it unsuitable to process reads from large genomes with commodity computers.
resultsWe present a novel algorithm that produces accurate correction results with much less memory compared with previous solutions. The algorithm, named BLoom-filter-based Error correction Solution for high-throughput Sequencing reads (BLESS), uses a single minimum-sized Bloom filter, and is also able to tolerate a higher false-positive rate, thus allowing us to correct errors with a 40× memory usage reduction on average compared with previous methods. Meanwhile, BLESS can extend reads like DNA assemblers to correct errors at the end of reads. Evaluations using real and simulated reads showed that BLESS could generate more accurate results than existing solutions. After errors were corrected using BLESS, 69% of initially unaligned reads could be aligned correctly. Additionally, de novo assembly results became 50% longer with 66% fewer assembly errors. AVAILABILITY AND IMPLEMENTATION: Freely available at http://sourceforge.net/p/bless-ec CONTACT: dchen@illinois.edu 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.