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RRAP: RPKM Recruitment Analysis Pipeline
Conner Y Kojima1, Eric W Getz1, J Cameron Thrash1
1Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.
Microbiology Resource Announcements
|August 22, 2022
Summary
We developed RRAP (RPKM Recruitment Analysis Pipeline) to automate metagenomic analysis. This pipeline quantifies microbial abundances using reads per kilobase per million (RPKM) normalization for accurate in situ microbial community profiling.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Quantifying microbial abundances in situ is crucial for understanding microbial communities.
- Metagenomic read recruitment to reference genomes is a common quantification method.
- Normalization using reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM) is standard practice.
Purpose of the Study:
- To automate the process of metagenomic read recruitment and RPKM normalization.
- To provide a user-friendly pipeline for microbial abundance quantification.
- To streamline in situ microbial community analysis.
Main Methods:
- Development of RRAP (RPKM Recruitment Analysis Pipeline).
- Utilizing Bowtie2 for read alignment.
- Employing SAMtools for sequence manipulation and quantification.
Main Results:
- RRAP successfully automates metagenomic read recruitment.
- The pipeline enables efficient RPKM normalization for microbial abundance.
- RRAP integrates Bowtie2 and SAMtools for a comprehensive analysis workflow.
Conclusions:
- RRAP simplifies and standardizes the quantification of microbial abundances in situ.
- The pipeline enhances the efficiency of metagenomic data analysis.
- RRAP is a valuable tool for researchers studying microbial communities.
