# Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates

*PRI Rank #14 · Topics and Trends in Most Cited Salmonella and Campylobacter epidemiology Papers, Class of 2026*

*Canonical URL: https://pri.pepkio.com/top-papers/salmonella-and-campylobacter-epidemiology/2026/rank-14*

| Field | Value |
| --- | --- |
| Rank | #14 |
| 18m citations | 26 |
| Journal | BMC Genomics |
| Year | 2024 |
| DOI | 10.1186/s12864-024-10582-x |
| Corresponding authors | Seth Commichaux |
| Institution | University of Maryland, United States |

**Ranking page:** [Topics and Trends in Most Cited Salmonella and Campylobacter epidemiology Papers, Class of 2026](https://pri.pepkio.com/top-papers/salmonella-and-campylobacter-epidemiology/2026)

**Paper link:** [10.1186/s12864-024-10582-x](https://doi.org/10.1186/s12864-024-10582-x)

## Topics

Oxford Nanopore sequencing · bacterial genome assembly · polishing tools · long-read polishing · short-read polishing · medaka · Racon · NextPolish · Pilon · Polypolish · POLCA · Salmonella Newport · outbreak source tracking · genome accuracy · homopolymer errors · indels · phylogenetic resolution · nanopore assembly errors

## Cite this ranking

```
Pepkio Research Index (PRI). Topics and Trends in Most Cited Salmonella and Campylobacter epidemiology Papers, Class of 2026. https://pri.pepkio.com/top-papers/salmonella-and-campylobacter-epidemiology/2026. Accessed 2026-07-24.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459
```