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RNA-seq analysisSoftwareTools

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Dr. Muniba Faiza
Last updated: March 23, 2023 12:42 pm
Dr. Muniba Faiza
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Pathonoia- A new tool to detect pathogens in RNA-seq data.
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Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].

Contents
How Pathonoia works?References

Pathonoia uses k-mer based method for species identification. It provides a nice framework that shows microbe-host interactions.

How Pathonoia works?

  • Pathonoia algorithm uses Kraken2 to align RNA-seq reads and to generate k-mer assignments and a taxonomic classification for each read.
  • It then combines all k-mer assignments of a sample into a non-read-count-based abundance metric.
  • Further, users are allowed to subject the output to downstream analysis that includes differential abundance analysis and differential expression analysis.
  • It finally outputs the potential effect of the organism in sample.

Pathonoia is capable of supporting novel hypotheses on microbial infections [1]. It is written in Python language and is freely available on GitHub.

For further reading, click here.


References

  1. Liebhoff, AM., Menden, K., Laschtowitz, A. et al. (2023). Pathogen detection in RNA-seq data with Pathonoia. BMC Bioinformatics 24, 53.
  2. Breitwieser, F. P., Baker, D. N., & Salzberg, S. L. (2018). KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome biology, 19(1), 1-10.
TAGGED:pathogen detectionpathonoiaRNA-seq
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ByDr. Muniba Faiza
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Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba
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