ArticleGenome biology2022
Strobealign: flexible seed size enables ultra-fast and accurate read alignment.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Computational tool choice impacts CRISPR spacer-protospacer detection.Bioinformatics (Oxford, England) · 2026Article
- Emerging investigator series: metagenomic insights into microbial controls of carbon cycling in alpine soils.Environmental science. Processes & impacts · 2026Article
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns.PLoS computational biology · 2026Article
- Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.bioRxiv : the preprint server for biology · 2026Article
- Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.medRxiv : the preprint server for health sciences · 2026Article
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.Microbiome · 2026Article
- Exploring Pinus nigra's induced defense arsenal against Diplodia sapinea through gene and metabolic pathway analysis.BMC genomics · 2026Article
- Short-read genome skimming enables molecular barcoding of old myxomycete collections.IMA fungus · 2026Article
- Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.Nature communications · 2025Article
- Density-reducing Jaccard estimators for sketch-based long read applications.BMC bioinformatics · 2025Article
- Microbial model communities exhibit widespread metabolic interdependencies.Communications biology · 2025Article
- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
- Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.Microbiome · 2025Article
- Evaluation of metagenome binning: advances and challenges.Briefings in bioinformatics · 2025Article
- Locityper enables targeted genotyping of complex polymorphic genes.Nature genetics · 2025Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers, in a novel seeding approach for constructing dynamic-sized fuzzy seeds and implement the method in a short-read aligner, strobealign. The seeding is fast to construct and effectively reduces repetitiveness in the seeding step, as shown using a novel metric E-hits. strobealign is several times faster than traditional aligners at similar and sometimes higher accuracy while being both faster and more accurate than more recently proposed aligners for short reads of lengths 150nt and longer. Availability: https://github.com/ksahlin/strobealign.
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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.