ArticleBMC bioinformatics2016
Read mapping on de Bruijn graphs.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
- The reference genome of the human diploid cell line RPE-1.Nature communications · 2025Article
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.Bioinformatics (Oxford, England) · 2024Article
- Pan-genome de Bruijn graph using the bidirectional FM-index.BMC bioinformatics · 2023Article
- Aligning distant sequences to graphs using long seed sketches.Genome research · 2023Article
- DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage.Computational and structural biotechnology journal · 2023Article
- Review
- From the reference human genome to human pangenome: Premise, promise and challenge.Frontiers in genetics · 2022Article
- Data Structures to Represent a Set ofACM computing surveys · 2022Article
- PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index.Bioinformatics (Oxford, England) · 2021Article
- Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotiferScience advances · 2021Article
- GraphAligner: rapid and versatile sequence-to-graph alignment.Genome biology · 2020Article
- SPAligner: alignment of long diverged molecular sequences to assembly graphs.BMC bioinformatics · 2020Article
- Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications.Bioinformatics (Oxford, England) · 2020Article
- Fast read alignment with incorporation of known genomic variants.BMC medical informatics and decision making · 2019Article
- Bit-parallel sequence-to-graph alignment.Bioinformatics (Oxford, England) · 2019Article
- Fully-sensitive seed finding in sequence graphs using a hybrid index.Bioinformatics (Oxford, England) · 2019Article
- BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs.BMC bioinformatics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig describes the sequence found along some path of the assembly graph, however, the set of contigs does not record all the sequence information contained in that graph. Although many subsequent analyses can be performed with the set of contigs, one may ask whether mapping reads on the contigs is as informative as mapping them on the paths of the assembly graph. Currently, one lacks practical tools to perform mapping on such graphs.
resultsHere, we propose a formal definition of mapping on a de Bruijn graph, analyse the problem complexity which turns out to be NP-complete, and provide a practical solution. We propose a pipeline called GGMAP (Greedy Graph MAPping). Its novelty is a procedure to map reads on branching paths of the graph, for which we designed a heuristic algorithm called BGREAT (de Bruijn Graph REAd mapping Tool). For the sake of efficiency, BGREAT rewrites a read sequence as a succession of unitigs sequences. GGMAP can map millions of reads per CPU hour on a de Bruijn graph built from a large set of human genomic reads. Surprisingly, results show that up to 22 % more reads can be mapped on the graph but not on the contig set.
conclusionsAlthough mapping reads on a de Bruijn graph is complex task, our proposal offers a practical solution combining efficiency with an improved mapping capacity compared to assembly-based mapping even for complex eukaryotic data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.