{"title":"Sama: a contig assembler with correctness guarantee.","authors":"Leena Salmela","doi":"10.1186/s13015-025-00280-y","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>In genome assembly the task is to reconstruct a genome based on sequencing reads. Current practical methods are based on heuristics which are hard to analyse and thus such analysis is not readily available.</p><p><strong>Results: </strong>We present a model for estimating the probability of misassembly at each position of a de Bruijn graph based assembly. Unlike previous work, our model also takes into account missing data. We apply our model to produce contigs with correctness guarantee and correctness estimates for each position in the contigs.</p><p><strong>Conclusions: </strong>Our experiments show that when the coverage of k-mers is high enough, our method produces contigs with similar contiguity characteristics as state-of-the-art assemblers which are based on heuristic correction of the de Bruijn graph. Our model may have further applications in downstream analysis of contigs or in any analysis working directly on the de Bruijn graph.</p>","PeriodicalId":50823,"journal":{"name":"Algorithms for Molecular Biology","volume":"20 1","pages":"9"},"PeriodicalIF":1.5000,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135590/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Algorithms for Molecular Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13015-025-00280-y","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
Background: In genome assembly the task is to reconstruct a genome based on sequencing reads. Current practical methods are based on heuristics which are hard to analyse and thus such analysis is not readily available.
Results: We present a model for estimating the probability of misassembly at each position of a de Bruijn graph based assembly. Unlike previous work, our model also takes into account missing data. We apply our model to produce contigs with correctness guarantee and correctness estimates for each position in the contigs.
Conclusions: Our experiments show that when the coverage of k-mers is high enough, our method produces contigs with similar contiguity characteristics as state-of-the-art assemblers which are based on heuristic correction of the de Bruijn graph. Our model may have further applications in downstream analysis of contigs or in any analysis working directly on the de Bruijn graph.
期刊介绍：
Algorithms for Molecular Biology publishes articles on novel algorithms for biological sequence and structure analysis, phylogeny reconstruction, and combinatorial algorithms and machine learning.
Areas of interest include but are not limited to: algorithms for RNA and protein structure analysis, gene prediction and genome analysis, comparative sequence analysis and alignment, phylogeny, gene expression, machine learning, and combinatorial algorithms.
Where appropriate, manuscripts should describe applications to real-world data. However, pure algorithm papers are also welcome if future applications to biological data are to be expected, or if they address complexity or approximation issues of novel computational problems in molecular biology. Articles about novel software tools will be considered for publication if they contain some algorithmically interesting aspects.
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