Background: Graph-based representation of genome assemblies has been recently used in different applications - from gene finding to haplotype separation. While most of these applications are based on the alignment of molecular sequences to assembly graphs, existing software tools for finding such alignments have important limitations. Results: We present a novel SPAligner (Saint Petersburg Aligner) tool for aligning long diverged molecular sequences to assembly graphs and demonstrate that SPAligner is an efficient solution for mapping third generation sequencing data and can also 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 at https://github.com/ablab/spades/releases/tag/spaligner-paper.
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