ArticleScientific reports2019
Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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
7 citing papers in PubMed.
- Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.Interdisciplinary sciences, computational life sciences · 2026Article
- A reinforcement learning approach to effective forecasting of pediatric hypoglycemia in diabetes I patients using an extended de Bruijn graph.Scientific reports · 2024Article
- LMAS: evaluating metagenomic short de novo assembly methods through defined communities.GigaScience · 2022Article
- Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing.BMC bioinformatics · 2022Article
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.Microbial genomics · 2020Review
- The parallelism motifs of genomic data analysis.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2020Article
- UniqueInternational journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Remarkable advancements in high-throughput gene sequencing technologies have led to an exponential growth in the number of sequenced genomes. However, unavailability of highly parallel and scalable de novo assembly algorithms have hindered biologists attempting to swiftly assemble high-quality complex genomes. Popular de Bruijn graph assemblers, such as IDBA-UD, generate high-quality assemblies by iterating over a set of k-values used in the construction of de Bruijn graphs (DBG). However, this process of sequentially iterating from small to large k-values slows down the process of assembly. In this paper, we propose ScalaDBG, which metamorphoses this sequential process, building DBGs for each distinct k-value in parallel. We develop an innovative mechanism to "patch" a higher k-valued graph with contigs generated from a lower k-valued graph. Moreover, ScalaDBG leverages multi-level parallelism, by both scaling up on all cores of a node, and scaling out to multiple nodes simultaneously. We demonstrate that ScalaDBG completes assembling the genome faster than IDBA-UD, but with similar accuracy on a variety of datasets (6.8X faster for one of the most complex genome in our dataset).
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Registered trials
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