POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy

Abstract Summary Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2024-03, Vol.40 (4)
Main Author: Hölzer, Martin
Format: Article
Language:English
Subjects:
Applications Note
Availability
Conserved sequence
Genomes
Proteins
Source code
Taxonomy
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Summary:Abstract Summary Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies. Availability and implementation The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btae175