POCP-nf

POCP-nf automates the calculation of the Percentage Of Conserved Proteins (POCP) for assessing prokaryote genus boundaries in bacterial taxonomy.

Key Features:

• DIAMOND alignment: The pipeline uses DIAMOND for faster protein alignments with sensitivity similar to BLASTP.
• Nextflow implementation: The pipeline is implemented in Nextflow, enabling reproducible and scalable workflow execution.
• Container and environment support: The pipeline supports Conda and Docker for dependency management and portability.
• Adaptable input: The open-source code can be adapted for various prokaryotic genome and protein datasets.

Scientific Applications:

• Bacterial taxonomic classification: POCP-nf calculates POCP values to assess prokaryote genus boundaries in taxonomic studies.
• Large-scale genome analysis: The pipeline handles the exponential increase in bacterial genomes enabled by sequencing technology advancements.

Methodology:

POCP-nf uses DIAMOND for protein alignments and is implemented in Nextflow.