ArticleiScience2020
HASLR: Fast Hybrid Assembly of Long Reads.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 67 citations in OpenAlex.
- Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.Microbial genomics · 2026Article
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- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
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- Benchmarking of bioinformatics tools for the hybridComputational and structural biotechnology journal · 2025Article
- Fusarium Genome Sequencing and Assembly.Methods in molecular biology (Clifton, N.J.) · 2025Article
- AssessingiScience · 2024Article
- Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.G3 (Bethesda, Md.) · 2024Article
- Chromosome-Level Reference Genome of the Ponza Grayling (Hipparchia sbordonii), an Italian Endemic and Endangered Butterfly.Genome biology and evolution · 2024Article
- Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.Microbiology (Reading, England) · 2024Article
- Genomic resources for the Yellowfin tuna Thunnus albacares.Molecular biology reports · 2024Article
- Comparative Genomic Analysis ofJournal of fungi (Basel, Switzerland) · 2023Article
- Mabs, a suite of tools for gene-informed genome assembly.BMC bioinformatics · 2023Article
- A practical assembly guideline for genomes with various levels of heterozygosity.Briefings in bioinformatics · 2023Article
- Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria.The ISME journal · 2023Article
- IntegratedNAR genomics and bioinformatics · 2023Article
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
- Article
- Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.F1000Research · 2023Review
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies. The larger effective length of their reads has provided a means to overcome the challenges of short to mid-range repeats. Currently, accurate long read assemblers are computationally expensive, whereas faster methods are not as accurate. Moreover, despite recent advances in third-generation sequencing, researchers still tend to generate accurate short reads for many of the analysis tasks. Here, we present HASLR, a hybrid assembler that uses error-prone long reads together with high-quality short reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on most of the samples, while being on par with other assemblers in terms of contiguity and accuracy.
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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.