ArticleBioinformatics (Oxford, England)2020
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats.
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 38 papers.
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Who cites it
38 citing papers in PubMed, 69 citations in OpenAlex.
- ChromoMapper: a new tool to quickly compare large genome assemblies.Bioinformatics advances · 2026Article
- Chromosome-scale, haplotype-resolved genome of Bighead catfish for conservation and aquaculture.Scientific data · 2025Article
- Genetic diversity and evolution of rice centromeres.Nature genetics · 2025Article
- Genome assembly of two allotetraploid cotton germplasms reveals mechanisms of somatic embryogenesis and enables precise genome editing.Nature genetics · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.Genome research · 2024Article
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.Cell genomics · 2024Article
- Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice.Nature communications · 2024Article
- Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae.BMC genomics · 2024Article
- Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly.Nature methods · 2024Article
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement.Genome research · 2024Article
- De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus.GigaScience · 2024Article
- Telomere-to-telomere assembly of diploid chromosomes with Verkko.Nature biotechnology · 2023Article
- UniAligner: a parameter-free framework for fast sequence alignment.Nature methods · 2023Article
- Article
- A survey of mapping algorithms in the long-reads era.Genome biology · 2023Review
- GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.Bioinformatics (Oxford, England) · 2023Article
- Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
motivationExtra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.
resultsTo address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres. AVAILABILITY AND IMPLEMENTATION: https://github.com/ablab/TandemTools. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.