ArticlePloS one2018
GRASShopPER-An algorithm for de novo assembly based on GPU alignments.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.PLoS computational biology · 2026Article
- ProProtein: A platform for fully automated identification of 3D structure fluctuations in MD simulation trajectories.PloS one · 2025Article
- Genome-scale de novo assembly using ALGA.Bioinformatics (Oxford, England) · 2021Article
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9 authors.
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Abstract
Next generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes a great computational challenge in accurately reconstructing a genome sequence de novo using these short sequences. Here, we propose the GRASShopPER assembler, which follows an approach of overlap-layout-consensus. It uses an efficient GPU implementation for the sequence alignment during the graph construction stage and a greedy hyper-heuristic algorithm at the fork detection stage. A two-part fork detection method allows us to identify repeated fragments of a genome and to reconstruct them without misassemblies. The assemblies of data sets of bacteria Candidatus Microthrix, nematode Caenorhabditis elegans, and human chromosome 14 were evaluated with the golden standard tool QUAST. In comparison with other assemblers, GRASShopPER provided contigs that covered the largest part of the genomes and, at the same time, kept good values of other metrics, e.g., NG50 and misassembly rate.
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