ArticleGenome research2024
Seamless, rapid, and accurate analyses of outbreak genomic data using split
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Persisting predominant clinical CC87Emerging microbes & infections · 2026Review
- BeyondEmerging microbes & infections · 2026Article
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- Alignment-freeJournal of clinical microbiology · 2026Article
- New isolates from the 1970s to early 2000s provide insights into the evolution ofMicrobial genomics · 2026Article
- Novel transposon TnMicrobial genomics · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Min-frame transformation enables more sensitive viral genome alignment.bioRxiv : the preprint server for biology · 2026Article
- Whole-genome sequencing of MDR K. pneumoniae circulating in Moroccan river ecosystems: a comprehensive genomic analysis of environmental isolates.BMC genomics · 2026Article
- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Observational
- Rapid and reproducible haplotyping of complete mitochondrial genomes using split k-mers.BMC genomics · 2026Article
- Probing Genomic Diversity ofFoods (Basel, Switzerland) · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay.bioRxiv : the preprint server for biology · 2026Article
- Genomic and pathogenic characterization of Listeria ivanovii subsp. londoniensis from ovine farms in China.BMC veterinary research · 2026Article
- Novel transposon TnmedRxiv : the preprint server for health sciences · 2026Article
- Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens.Microbial genomics · 2026Article
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split
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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.