ArticleBMC bioinformatics2012
Exploiting sparseness in de novo genome assembly.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
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- Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire.BMC genomics · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Parasite manipulation of host phenotypes inferred from transcriptional analyses in a trematode-amphipod system.Molecular ecology · 2023Article
- Genome assembly in the telomere-to-telomere era.ArXiv · 2023Article
- 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication.Plants (Basel, Switzerland) · 2023Article
- N6-methyladenosine participates in mouse hippocampus neurodegeneration via PD-1/PD-L1 pathway.Frontiers in neuroscience · 2023Article
- Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata.BMC biology · 2022Article
- Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data.MicrobiologyOpen · 2022Review
- Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.Cell systems · 2021Article
- Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod.Heredity · 2021Article
- Sequence-specific minimizers via polar sets.Bioinformatics (Oxford, England) · 2021Article
- Metagenome SNP calling via read-colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2021Article
- Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- The first Conus genome assembly reveals a primary genetic central dogma of conopeptides in C. betulinus.Cell discovery · 2021Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.
methodsIn this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer.
resultsWe implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.
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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.