ReviewGenome biology2023
A survey of mapping algorithms in the long-reads era.
Review in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed.
- Review
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of Viola philippica (Malpighiales, Violaceae).Planta · 2026Article
- Comparative analysis of mitochondrial genomes of Iris lactea reveals gene transfer and RNA-editing events.Molecular biology reports · 2026Article
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- Integrative analysis of in silico predictions and clinical evidence to delineate the capability of HiFi long-read sequencing in paralogous genes.NPJ genomic medicine · 2026Article
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Mitogenome assembly and phylogenetic relationships ofFrontiers in plant science · 2026Article
- The complete mitochondrial genome and phylogenetic analysis ofFrontiers in plant science · 2026Article
- Article
- Density-reducing Jaccard estimators for sketch-based long read applications.BMC bioinformatics · 2025Article
- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- Complete mitochondrial genome assembly and structural feature analysis of Thinopyrum elongatum (Poaceae).Planta · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.Research square · 2025Article
- Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.bioRxiv : the preprint server for biology · 2025Article
- Panaln: indexing pangenome for read alignment.Bioinformatics (Oxford, England) · 2025Article
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Mitochondrial genome assembly of the Chinese endemic species of Camellia luteoflora and revealing its repetitive sequence mediated recombination, codon preferences and MTPTs.BMC plant biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a seed-and-chain framework due to the seed abundance in each read. The main novelties are based on alternative seed constructs or chaining formulations. Dozens of tools now exist, whose heuristics have evolved considerably. We provide an overview of the methods used in long-read mappers. Since they are driven by implementation-specific parameters, we develop an original visualization tool to understand the parameter settings ( http://bcazaux.polytech-lille.net/Minimap2/ ).
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Registered trials
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.