ArticleBioinformatics (Oxford, England)2019
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- TELLBASE: a novel tool of TELL-seq barcode-assisted scaffold assembler for bacterial genomes.Briefings in bioinformatics · 2025Article
- Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.Functional & integrative genomics · 2025Review
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.Nature communications · 2024Article
- cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data.Bioinformatics (Oxford, England) · 2024Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads.iMeta · 2022Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Characterization and phylogenetic analysis of the mitochondrial genome sequence ofMitochondrial DNA. Part B, Resources · 2022Article
- Article
- SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.BMC bioinformatics · 2021Article
- Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content.iScience · 2021Article
- A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.Computational and structural biotechnology journal · 2021Review
- Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.BMC bioinformatics · 2020Article
- Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.Genome research · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
motivationThe recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly.
resultsWe describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed. AVAILABILITY AND IMPLEMENTATION: Source code and installation manual for cloudSPAdes are available at https://github.com/ablab/spades/releases/tag/cloudspades-paper. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.