POLARtron Analysis (PA) Pipeline

Contents

• Installation
• Detailed Guide
  • Usage and options
  • Directory structure

Installation

The POLARtron Analysis (PA) pipeline and all its dependencies are Linux based, typically running under Linux operating system, preferably (but not necessarily) on a computer cluster. The included test set can run on a laptop in under 5 minutes. There are several options for installation, detailed below.

Install PAP

Download the PAP repository from Github

git clone https://github.com/peradastra/PAP.git

or...

curl -sSL -o PAP.zip https://github.com/peradastra/PAP/master.zip && \
mkdir -p PAP && \
unzip PAP.zip -d PAP

Install dependencies to run PAP

If you already have a Anaconda/Miniconda installation then you can create a conda environment using the provided
environment definition.

1. Create the conda environment

conda env create -n pap_conda_env -f PAP/pap_conda_env.yml

2. Activate PAP conda environment

conda activate pap_conda_env

Test PAP installation

cd PAP && \
bash run_pap.sh -d Library001

Detailed Guide

Usage and options

Usage: run_pap.sh [-d TOP_DIR] [-t THREADS] -h
        -d  Top level directory which must contain a subdirectory (fastq/) with fastq files
        -t  Number of threads for BWA alignment (Default: 16)
        -h  Print this help and exit

Directory structure

Place the paired-end sequenced reads in a folder labeled fastq. For example, if your experiment is called "Library001", you should have a folder labeled "Library001," and it should contain one subfolder labeled "fastq" with the fastq files in it. The fastqs can be zipped or unzipped, and there can be multiple pairs. This directory structure is shown below in the form of a tree structure.

Library001
└── fastq
    ├── library001_R1.fastq.gz
    └── library001_R2.fastq.gz

The pipeline will create an "aligned" folder, an "debug" folder and a "final" folder under "Library001." The "alignments" folder will contain alignments. The "debug" folder will contain the error and log files. The "final" folder will contain the final results of the pipeline.

Library001
├── fastq
│   ├── library001_R1.fastq.gz
│   └── library001_R2.fastq.gz
└── pap
    ├── aligned
    │   ├── all_alignment_stats.txt
    │   ├── classified_alignments.bam
    │   └── viral_alignment_stats.txt
    ├── debug
    │   ├── align.out
    │   ├── all_stats.out
    │   ├── dedup.out
    *   *
    *   *
    *   *
    │   ├── matefix.out
    │   ├── recombo.out
    │   ├── sort.out
    │   └── viral_stats.out
    └── final
        ├── qc_stats.txt
        └── result.csv