The Hydrostructure：一个安全完整的基因组组装算法的通用框架
The Hydrostructure: a Universal Framework for Safe and Complete Algorithms for Genome Assembly
摘要：
基因组组装是生物信息学中的一个基本问题，需要从由一组读取（从基因组测序的短字符串）构建的组装图重建源基因组。基因组组装解的概念是图的弧覆盖行走。由于组装图允许许多解决方案，目标是找到在所有解决方案中明确存在的东西，或者什么是安全的。大多数实际的汇编程序都是基于在其核心unitigs的算法，即路径的内部节点有单位的入度和出度，并且显然是安全的。找到解决方案的所有安全部分的长期开放问题最近得到解决[RECOMB 2016]，重叠群长度增加了60%。这种安全和完整的基因组组装算法之后，其他工作改善了时间界限，以及扩展了不同概念的组装解决方案的结果。但它仍然开放是否可以完整的基因组组装模型的实际适用性。在本文中，我们提出了一个通用的框架，以获得安全和完整的算法，统一了以前的结果，同时也允许容易概括的组装问题，包括许多实际方面。这是基于一种新的图形结构，称为行走的水力结构，它突出了从行走的角度来看图形的可达性。水力结构允许现有的安全走道的简单特征，以及它们的新的实用版本。几乎所有的特征都直接适用于最佳验证算法和简单的枚举算法。这些算法中的大多数还使用增量计算过程和特定模型的先前最优算法来改进最优性。
英文摘要：
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of an arc-covering walk of the graph. Since assembly graphs admit many solutions, the goal is to find what is definitely present in all solutions, or what is safe. Most practical assemblers are based on heuristics having at their core unitigs, namely paths whose internal nodes have unit in-degree and out-degree, and which are clearly safe. The long-standing open problem of finding all the safe parts of the solutions was recently solved [RECOMB 2016] yielding a 60% increase in contig length. This safe and complete genome assembly algorithm was followed by other works improving the time bounds, as well as extending the results for different notions of assembly solution. But it remained open whether one can be complete also for models of genome assembly of practical applicability. In this paper we present a universal framework for obtaining safe and complete algorithms which unify the previous results, while also allowing for easy generalisations to assembly problems including many practical aspects. This is based on a novel graph structure, called the hydrostructure of a walk, which highlights the reachability properties of the graph from the perspective of the walk. The hydrostructure allows for simple characterisations of the existing safe walks, and of their new practical versions. Almost all of our characterisations are directly adaptable to optimal verification algorithms, and simple enumeration algorithms. Most of these algorithms are also improved to optimality using an incremental computation procedure and a previous optimal algorithm of a specific model.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
