ArticleBMC bioinformatics2020
SPAligner: alignment of long diverged molecular sequences to assembly graphs.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs.Microorganisms · 2024Article
- Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.Bioinformatics (Oxford, England) · 2024Article
- Co-linear chaining on pangenome graphs.Algorithms for molecular biology : AMB · 2024Article
- Pan-genome de Bruijn graph using the bidirectional FM-index.BMC bioinformatics · 2023Article
- Chaining for accurate alignment of erroneous long reads to acyclic variation graphs.Bioinformatics (Oxford, England) · 2023Article
- Article
- Review
- From the reference human genome to human pangenome: Premise, promise and challenge.Frontiers in genetics · 2022Article
- Population-scale genotyping of structural variation in the era of long-read sequencing.Computational and structural biotechnology journal · 2022Review
- SAUTE: sequence assembly using target enrichment.BMC bioinformatics · 2021Article
- ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs.Microbiome · 2021Article
- Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms.Frontiers in microbiology · 2021Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGraph-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.
resultsIn 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.
conclusionsOur 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.
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