ArticleGenome research2004
De novo repeat classification and fragment assembly.
Article in Genome research, 2004. 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 84 papers.
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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
84 citing papers in PubMed.
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction.Bioinformatics (Oxford, England) · 2024Article
- Maximum-scoring path sets on pangenome graphs of constant treewidth.Frontiers in bioinformatics · 2024Article
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.Bioinformatics (Oxford, England) · 2023Article
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.bioRxiv : the preprint server for biology · 2023Article
- Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.Nature methods · 2023Article
- Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing.Sensors (Basel, Switzerland) · 2023Article
- Phased Genome Assemblies.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.Frontiers in genetics · 2023Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Fast characterization of segmental duplication structure in multiple genome assemblies.Algorithms for molecular biology : AMB · 2022Article
- KOMB: K-core based de novo characterization of copy number variation in microbiomes.Computational and structural biotechnology journal · 2022Article
- Article
- Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.Cell systems · 2021Article
- Haploflow: strain-resolved de novo assembly of viral genomes.Genome biology · 2021Article
- Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs.Nature communications · 2021Article
- QAlign: aligning nanopore reads accurately using current-level modeling.Bioinformatics (Oxford, England) · 2021Article
- Efficient hybrid de novo assembly of human genomes with WENGAN.Nature biotechnology · 2021Article
- Haploflow: Strain-resolvedbioRxiv : the preprint server for biology · 2021Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issuedPevzner, Paul A [corrected to Pevzner, Pavel A]
Authors and funding
4 authors.
Funding
Abstract
Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats. Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes.
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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.