ammaraziz/metaphlan_pipeline

custom metaphlan pipeline for PBS schedular

MetaPhlan pipeline for automated submission of jobs to PBS schedular

This pipeline will run MetaPhlan and then StrainPhlan to detect species specific markers in sequencing data.

Usage

To run the script, simple call:

./stp.sh 

.fastq files are automatically detected and ran through the pipeline. Note, MetaPhlan/StrainPhlan does not handle paired end reads. Either combine fastq files or run each pair as a single.

Issues

When generating the marker files for Strainphlan, metaphlan detects Bm and Bp when the samples only contain Bp.

The workaround for this is to recode all Bm samples as actually Bp. This can be done by using the pickle package in python and readingi n the .pkl file. Code is found in modify_pkl.py

Once this is done, the new .pkl file needs to be stored in it's own folder in metaphlan.

To do

• MetaPhlan/StrainPhlan .py paths need to be soft-coded
• Add ExtractMarkers.py step to pipeline
• Add step to generate PCA plot