ArticleNucleic acids research2017
Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.BMC bioinformatics · 2025Article
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- AutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment.PloS one · 2025Article
- Identification of conserved genomic signatures specific to3 Biotech · 2023Article
- Genomic Characterization ofFrontiers in microbiology · 2022Article
- Development of reverse-transcriptase, real-time PCR assays to distinguish the Southern African Territories (SAT) serotypes 1 and 3 and topotype VII of SAT2 of Foot-and-Mouth Disease Virus.Frontiers in veterinary science · 2022Article
- Comparative Genomic and Transcriptomic Analysis of Naegleria fowleri Clinical and Environmental Isolates.mSphere · 2021Article
- Mining Public Metagenomes for Environmental Surveillance of Parasites: A Proof of Principle.Frontiers in microbiology · 2021Article
- Rapid and AccurateFrontiers in microbiology · 2021Article
- Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants.BMC microbiology · 2020Article
- Identification of genetic relationships and subspecies signatures in Xylella fastidiosa.BMC genomics · 2019Article
- A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.PLoS computational biology · 2018Article
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Authors and funding
23 authors.
Funding
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Abstract
The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real datasets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci. The software is available for download at: http://github.com/phac-nml/neptune.
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