SPAligner: alignment of long diverged molecular sequences to assembly graphs
SPAligner: alignment of long diverged molecular sequences to assembly graphs
复制标题
DOI：
10.1186/s12859-020-03590-7
复制
发表时间：
2020-07-24
影响因子：
3
通讯作者：
Nurk, Sergey
中科院分区：
文献类型：
--
作者：
Dvorkina, Tatiana;Antipov, Dmitry;Nurk, Sergey
背景 基于图形的基因组组装表示最近已在不同的环境中使用 - 从改进的质粒序列重建和宏基因组数据的精细分析到读取纠错和无参考单倍型重建。虽然许多这些应用程序大量利用长核苷酸序列与组装图的比对，但用于查找此类比对的第一个通用软件工具最近才发布，其缺陷和局限性仍有待发现。此外，现有工具无法进行氨基酸序列比对，而这在各种情况下可能是有用的，特别是宏基因组测序数据的分析。结果在这项工作中，我们提出了一种新颖的 SPAligner（圣彼得堡对齐器）工具，用于将长分歧的核苷酸和氨基酸序列与组装图对齐。我们证明 SPAligner 是将第三代测序读段映射到各种复杂性的组装图上的有效解决方案，并展示了它如何促进复杂宏基因组数据集中已知基因的识别。结论我们的工作将有助于加速基于图的方法的开发，以解决序列与基因组组装比对问题。 SPAligner 作为 SPAdes 工具库的一部分实现，可在 Github 上获取。
Background Graph-based representation of genome assemblies has been recently used in different contexts - from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correction and reference-free haplotype reconstruction. While many of these applications heavily utilize the alignment of long nucleotide sequences to assembly graphs, first general-purpose software tools for finding such alignments have been released only recently and their deficiencies and limitations are yet to be discovered. Moreover, existing tools can not perform alignment of amino acid sequences, which could prove useful in various contexts - in particular the analysis of metagenomic sequencing data. Results In this work we present a novel SPAligner (Saint-Petersburg Aligner) tool for aligning long diverged nucleotide and amino acid sequences to assembly graphs. We demonstrate that SPAligner is an efficient solution for mapping third generation sequencing reads onto assembly graphs of various complexity and also show how it can facilitate the identification of known genes in complex metagenomic datasets. Conclusions Our work will facilitate accelerating the development of graph-based approaches in solving sequence to genome assembly alignment problem. SPAligner is implemented as a part of SPAdes tools library and is available on Github.