ArticleBioinformatics (Oxford, England)2014
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
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- Genomic Analyses ofJournal of fungi (Basel, Switzerland) · 2021Article
- Draft Genome Sequences of the Clinical Isolates Kp 23 and KPM 20.Microbiology resource announcements · 2021Article
- A Novel Polyvalent Bacteriophage vB_EcoM_swi3 Infects PathogenicFrontiers in microbiology · 2021Article
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- Plant Growth-Promoting Methylobacteria Selectively Increase the Biomass of Biotechnologically Relevant Microalgae.Frontiers in microbiology · 2020Article
- lptG contributes to changes in membrane permeability and the emergence of multidrug hypersusceptibility in a cystic fibrosis isolate of Pseudomonas aeruginosa.MicrobiologyOpen · 2019Article
- Genetic and Genome Analyses Reveal Genetically Distinct Populations of the Bee Pathogen Nosema ceranae from Thailand.Microbial ecology · 2019Article
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3 authors.
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Abstract
motivationDe novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies by guiding them with genomes from related species.
resultsHere we introduce AlignGraph, an algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. It aligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph. The incorporated positional information from the alignments and PE reads allows us to extend the initial assemblies, while avoiding incorrect extensions and early terminations. In our performance tests, AlignGraph was able to substantially improve the contigs and scaffolds from several assemblers. For instance, 28.7-62.3% of the contigs of Arabidopsis thaliana and human could be extended, resulting in improvements of common assembly metrics, such as an increase of the N50 of the extendable contigs by 89.9-94.5% and 80.3-165.8%, respectively. In another test, AlignGraph was able to improve the assembly of a published genome (Arabidopsis strain Landsberg) by increasing the N50 of its extendable scaffolds by 86.6%. These results demonstrate AlignGraph's efficiency in improving genome assemblies by taking advantage of closely related references. AVAILABILITY AND IMPLEMENTATION: The AlignGraph software can be downloaded for free from this site: https://github.com/baoe/AlignGraph.
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