GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach
BACKGROUND: Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. RESULTS: GraphSNP is an interacti...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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NLM (Medline)
2023
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| Subjects: | |
| Online Access: | View Fulltext in Publisher View in Scopus |
| LEADER | 01832nam a2200217Ia 4500 | ||
|---|---|---|---|
| 001 | 10.1186-s12859-023-05332-x | ||
| 008 | 230529s2023 CNT 000 0 und d | ||
| 020 | |a 14712105 (ISSN) | ||
| 245 | 1 | 0 | |a GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach |
| 260 | 0 | |b NLM (Medline) |c 2023 | |
| 856 | |z View Fulltext in Publisher |u https://doi.org/10.1186/s12859-023-05332-x | ||
| 856 | |z View in Scopus |u https://www.scopus.com/inward/record.uri?eid=2-s2.0-85159643599&doi=10.1186%2fs12859-023-05332-x&partnerID=40&md5=743222c63204ffff87d9e9236a8ba4d3 | ||
| 520 | 3 | |a BACKGROUND: Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. RESULTS: GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings. CONCLUSIONS: GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com . © 2023. The Author(s). | |
| 650 | 0 | 4 | |a Cluster and transmission analysis |
| 650 | 0 | 4 | |a Genomic epidemiology |
| 650 | 0 | 4 | |a SNP distance |
| 650 | 0 | 4 | |a Visualisation |
| 700 | 1 | 0 | |a Beatson, S.A. |e author |
| 700 | 1 | 0 | |a Forde, B.M. |e author |
| 700 | 1 | 0 | |a Permana, B. |e author |
| 773 | |t BMC bioinformatics | ||