- Introduction
- Software Requirement and Dependency
- Installation guide
- Basic Usage
- Batch Processing
- Example dataset
Microbial Index of Pathogenic bacteria (MIP) is an easy-to-use bioinformatic package that calculates the quantitative microbial pathogenic risk. MIP assesses the disease risk to human from a microbiome sample and reports the quantitative indices from multiple aspects using a reference pathogen database and an artificially curated pathogen-disease interaction network. MIP works as a plug-in tools of Parallel-META 3, and supports 16S rRNA amplicon sequences as input.
MIP requires Parallel-Meta-Suite, please refer to https://github.com/qdu-bioinfo/parallel-meta-suite#installation-guide for installation.
a. Download the package
git clone https://github.com/qdu-bioinfo/mip.git
b. Install by installer
cd mip
source install.sh
The package should take less than 1 minute to install on a computer with the specifications recommended above.
The example dataset could be found at “example” folder. Check the “example/Readme” for details about the demo run.
With a input 16S rRNA amplicon sequence file, e.g. sample1.fasta:
a. Profiling by Parallel-META using MIP database
PM-parallel-meta -r sample1.fasta -D P -f F -o sample1.out
The “sample1.out” folder is the profiling result.
b. Parse out the microbial index of pathogenic bacteria
PM-parse-mip -i sample1.out/classification.txt -o sample1.mip
The output contains 5 files：
sample1.mip.summary.out: The overall MIP;
sample1.mip.taxa.out: The relative abundance of species contributed to the overall MIP (MIP LV1);
sample1.mip.OTU.Abd.out: The relative abundance of reference OTUs contributed to the overall MIP (MIP LV1);
sample1.mip.infection.out: Human diseases associated with the identified pathogenic bacteria (MIP LV2);
sample1.mip.site.out: Targeted human organs or body sites (MIP LV3).
MIP also supports the batch input of profiling results by the following alternative two forms (compatible with Parallel-META 3):
a. Sample list
PM-parse-mip -l samples.list -o samples.mip
in which parameter “-l” assigns the file list of profiling results of multiple samples. The format of a sample list:
Sample1 /home/data/sample1.out/classification.txt
Sample2 /home/data/sample2.out/classification.txt
...
SampleN /home/data/sampleN.out/classification.txt
b. Abundance tables
PM-parse-mip -T samples.OTU.Abd -o samples.mip
in which parameter “-T” assigns the profiling result of OTU table of multiple samples. The format of a OTU table:
OTU_1 OTU_2 OTU_3 … OTU_M
Sample1 100 200 0 … 50
Sample2 0 300 600 … 100
… … … … … 60
SampleN 50 80 0 … 200
Here we provide a demo dataset with profiling results of 20 microbiome. To run the demo, you can either run the script “Readme”:
cd example
sh Readme
or type the following command:
PM-parse-mip -l samples.list -o samples.mip