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IPD2.0- An Updated Version of IPD to Analyze the SARS-CoV-2 Genome

Tariq Abdullah

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IPD2.0- An Updated Version of IPD to Analyze the SARS-CoV-2 Genome

IPD2.0 [1] is an updated version of the Infectious Pathogen Detector (IPD) [2]. It helps in deriving insights from the SARS-CoV-2 genome.

IPD is a computational pipeline that consists of an analysis module of SARS-CoV-2. This module performs genomic analysis that helps in understanding the dynamics and variability of the virus. The clade prediction accuracy of IPD2.0 is 92.8% [1]. IPD2.0 automatically upgrades the variant database using genome sequences from GISAID.

The SARS-CoV-2 module generates SARS-CoV-2 genomic samples and works on phylogenetic clade analysis. The users have to input Fastq files, sequencing type, molecular type, email address, and project name. The intermediate files can only be accessed using the desktop version of IPD2.0

IPD2.0 is freely accessible at http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html along with a web application available at http://ipd.actrec.gov.in/ipdweb/. It is written in Python3 and the desktop version is available for Linux requiring Conda and Tkinter for its installation.

For more details, read here.


References

  1. Desai, S., Rane, A., Joshi, A. et al. (2021). IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome. BMC Bioinformatics 22, 247.
  2. Desai, S., Rashmi, S., Rane, A., Dharavath, B., Sawant, A., & Dutt, A. (2021). An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Briefings in bioinformatics22(2), 1065-1075.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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