ArticleBioinformatics (Oxford, England)2024
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed.
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- A new core-genome MLST approach for Chlamydia trachomatis genomic surveillance and research.Nature communications · 2026Article
- Genomic signatures of dairy adaptation inProceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Comparative Genomics-Based Evaluation ofJournal of microbiology and biotechnology · 2026Article
- Clinical Emergence and Genomic Characterization of Aztreonam-Avibactam-ResistantAntibiotics (Basel, Switzerland) · 2026Article
- Novel Hawai'i and Pacific Island circulating clusters ofApplied and environmental microbiology · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Documenting Environmentally Acquired Mycobacterium intracellulare subsp. chimaera Pulmonary Disease Soon After Bronchiectasis Onset.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Clinical Characteristics and Molecular Epidemiology of Invasive NontypeableOpen forum infectious diseases · 2026Article
- Genomic characterization of multidrug-resistant Klebsiella pneumoniae clinical isolates from India.Scientific reports · 2026Article
- Pan-genome insights into genetic diversity, evolutionary dynamics, and pathogenic traits of Staphylococcus agnetis.BMC genomics · 2026Article
- Integrated analysis of transposon insertion sequencing and pangenome reveals core and lineage-specific essential genes inMicrobial genomics · 2026Article
- Dissemination of antimicrobial resistance in Klebsiella spp. from urban aquatic environments: a multi-country genomic perspective.Journal of advanced research · 2026Article
- Min-frame transformation enables more sensitive viral genome alignment.bioRxiv : the preprint server for biology · 2026Article
- Genomic characterization of an extensively drug-resistant Klebsiella pneumoniae co-harboring mcr-3.11, blaNDM-5 and blaCTX-M-27 isolated from pelvic effusion in a colon cancer patient.BMC microbiology · 2026Article
- Unraveling Cefiderocol Resistance in NDM- and OXA-48-like Co-ProducingAntibiotics (Basel, Switzerland) · 2026Article
- Clinical and genomic determinants associated with emergent ceftazidime-avibactam plus aztreonam non-susceptibility in ceftazidime-avibactam resistantAntimicrobial agents and chemotherapy · 2026Article
- Genomic and statistical models to characterizeMicrobial genomics · 2026Article
7 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
motivationSince 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the input to numerous downstream comparative analysis methods. Parsnp is one of the few multiple genome alignment methods able to scale to the current era of genomic data; however, there has been no major release since its initial release in 2014.
resultsTo address this gap, we developed Parsnp v2, which significantly improves on its original release. Parsnp v2 provides users with more control over executions of the program, allowing Parsnp to be better tailored for different use-cases. We introduce a partitioning option to Parsnp, which allows the input to be broken up into multiple parallel alignment processes which are then combined into a final alignment. The partitioning option can reduce memory usage by over 4× and reduce runtime by over 2×, all while maintaining a precise core-genome alignment. The partitioning workflow is also less susceptible to complications caused by assembly artifacts and minor variation, as alignment anchors only need to be conserved within their partition and not across the entire input set. We highlight the performance on datasets involving thousands of bacterial and viral genomes. AVAILABILITY AND IMPLEMENTATION: Parsnp v2 is available at https://github.com/marbl/parsnp.
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