ArticleGenome biology2014
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,091 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
1,091 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- O‑Island 28 encodes a type I secretion and RTX adhesion system regulated by RstA and required for early EHEC O157:H7 adherence.Gut microbes · 2026Article
- Emergence, climate-driven expansion, and diversification of a EuropeanEmerging microbes & infections · 2026Article
- Emergence ofVirulence · 2026Article
- Smaller Genomes and Shorter Prophage Sequences Differentiate Clinical from Environmental Isolates ofbioRxiv : the preprint server for biology · 2026Article
- Phenotypic and phylogenomic characterization of Lactococcus garvieae isolates from rainbow trout (Oncorhynchus mykiss) in Türkiye.Veterinary research communications · 2026Article
- Whole genome ofMicrobiology resource announcements · 2026Article
- Protein kinase F regulates the virulence ofInfection and immunity · 2026Article
- A standardized workflow for typing S. marcescens outbreaks using FT-IR spectroscopy.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Performance of the IR Biotyper, Nanopore, and Illumina sequencing to discriminateMicrobiology spectrum · 2026Article
- Metagenomic insights into pathogen diversity and public health risk of Haemaphysalis longicornis in Gansu Province of China.PLoS neglected tropical diseases · 2026Article
- Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa.PLoS pathogens · 2026Article
- Genomic Characterization of a Multidrug-Resistant Serratia marcescens Isolate Recovered from a Neonatal Meningitis Case in Iraq.Current microbiology · 2026Article
- Prevalence, genomic characterization, and biofilm-forming capacity of extended-spectrum β-lactamase-producing Escherichia coli from faecal samples of broiler chickens in Jinan City, China.Poultry science · 2026Article
- Genome features and antimicrobial resistance ofMicrobiology spectrum · 2026Article
- Intraspecific diversity ofMicrobiology spectrum · 2026Article
- Lineage-associated differences in adenine methylation patterns of mammalian-associatedMicrobiology spectrum · 2026Article
- Effector loss and gain drives host range at a fitness cost.PLoS pathogens · 2026Article
- Multiple Independent Origins of TnAntibiotics (Basel, Switzerland) · 2026Article
- Escherichia coli ST131 Drives Carbapenem Use for E. coli Bloodstream Infections.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
1,031 more citing papers are in PubMed but not listed here.
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
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.
Indexed as
Identifiers
What OpenQuestion holds
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.