ArticleBioinformatics (Oxford, England)2012
Fulcrum: condensing redundant reads from high-throughput sequencing studies.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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.
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Who cites it
20 citing papers in PubMed.
- Fastq-dupaway: a fast and memory-efficient tool for deduplication of single- and paired-end NGS data.Scientific reports · 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
- Fast-HBR: Fast hash based duplicate read remover.Bioinformation · 2022Article
- Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations.Scientific reports · 2021Article
- Ultra-Deep Massive Parallel Sequencing of Plasma Cell-Free DNA Enables Large-Scale Profiling of Driver Mutations in Vietnamese Patients With Advanced Non-Small Cell Lung Cancer.Frontiers in oncology · 2020Article
- NGSReadsTreatment - A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data.Scientific reports · 2019Article
- Article
- Conducting metagenomic studies in microbiology and clinical research.Applied microbiology and biotechnology · 2018Review
- AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.Bioinformatics (Oxford, England) · 2018Article
- miR-181a-5p Regulates TNF-α and miR-21a-5p Influences Gualynate-Binding Protein 5 and IL-10 Expression in Macrophages Affecting Host Control ofFrontiers in immunology · 2018Article
- Effect of method of deduplication on estimation of differential gene expression using RNA-seq.PeerJ · 2017Article
- Removing duplicate reads using graphics processing units.BMC bioinformatics · 2016Article
- Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy.Journal of evolutionary biology · 2016Article
- Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini).BMC evolutionary biology · 2015Article
- Reference-based compression of short-read sequences using path encoding.Bioinformatics (Oxford, England) · 2015Article
- Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata.Genome announcements · 2015Article
- G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods.Frontiers in bioengineering and biotechnology · 2015Article
- Oculus: faster sequence alignment by streaming read compression.BMC bioinformatics · 2012Article
- Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida.BMC genomics · 2012Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationUltra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and costs.
resultsWe developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.
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.