EVAtool

Quick start

If you would like to get start using EVAtool, please following the any of the follwing document.

• Quick start from PyPI
• Quick start from Docker

Introduction

EVAtool (EV analysis tool) is a state-of-the-art tool for quantification and abundance of small ncRNA-seq dataset in EVs. In EVAtool, we collected seven ncRNA types (miRNA, snoRNA, piRNA, snRNA, rRNA, tRNA and Y RNA) references as default to evaluate the abundence of each small ncRNA in EVs.

With current newest dependences (mainly bowtie2, samtool, fastq-dump, bedtools and trimmomatic-0.39.jar) and high-performance algorithm RDAA (Reads Dynamic Assignment Algorithm), the tool is perfectly capable of processing small RNA-seq data from small EVs (sEVs) or large EVs (lEVs). It is also capable of processing other RNA-seq data (such as long ncRNA data) with minor modifications to the command-line call. Finally, EVAtool visualized the main results and supports the online report.

EVAtool has been implemented in Python >=3.5, Jupyter and HTML.

Table of Contents

• System Requirements
• Python
  • Installation with pip
  • Installation from source
  • Quick Start by pip
• Docker
  • Installation
  • Quick Start by docker
• Advanced option
• Directory tree
• Help

System Requirements

• Windows (>= 7), Mac OS X (>= 10.8) or Linux
• Python >= 3.5
• JDK 8

All other software dependencies are installed automatically when installing EVAtool. Some softwares versions are as follows:

• samtools = 1.12
  
• bowtie2 = 2.4.2
  
• fastq-dump = 2.10.9
  
• trimmomatic-0.39.jar
  
• bedtools = 2.30.0
  

Python

Installation with pip

The Python version of EVAtool can be installed by running the following from a terminal:

pip install EVAtool

Installation of EVAtool and all dependencies should take no more than one minutes.

Installation from source

The Python version of PHATE can be installed from GitHub by running the following from a terminal:

git clone --recursive git@github.com:xieguiyan/EVAtool.git
cd EVAtool/
python setup.py install --user

Quick Start by pip

To begin, the human genome and seven types references needed to be download from http://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zip and unzip it into the working directory.

mkdir ~/evatool_work
cd ~/evatool_work
wget "http://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zip"
unzip refs.zip

If you have already prepared the data file (SRA, FASTQ or zipped FASTQ format) you can run EVAtool as follows (Here we use example.fastq.gz data as an example):

wget "http://bioinfo.life.hust.edu.cn/EVAtool/example/example.fastq.gz"
evatool \
-i example.fastq.gz
-o {directory for output or .}

EVAtool accepts the following data types: example.sra, example.fastq and example.fastq.gz.

Docker

Installation

The docker image of evatool can be accessed by running the following from a terminal:

docker pull guobioinfolab/evatool

Then, prepare reference data and sequence data like the pip part:

mkdir ~/evatool_work
cd ~/evatool_work
wget "http://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zip"
unzip refs.zip
wget "http://bioinfo.life.hust.edu.cn/EVAtool/example/example.fastq.gz"

Quick Start by docker

Take the example.fastq.gz as example:

docker run -it -v $PWD:/work_path -w /work_path guobioinfolab/evatool -i example.fastq.gz -o .

Advanced option

1. Custom ncRNA type(s)

   • Based on existing reference sequences

     • change the input parameter of ncRNA type list, the default ncRNAs are include 7 types: "miRNA" "rRNA" "tRNA" "piRNA" "snoRNA" "snRNA" "YRNA".

   • Add other type reference sequences

     • Three steps :
     1. Add the ncRNA reference and index into refs;

     mkdir [ncRNA name]
     add the reference and index to the directory
     

     2. Change the input parameter of ncRNA type list;

     -n  "miRNA" "rRNA" "tRNA"
     

     3. Add the ncRNA name and reference directory in config file as following the existing ways.

     "miRNA_index": "/refs/miRNA/hsa.hairpin.fa"
     

Directory tree

├── bin
│   ├── bedtools
│   ├── bowtie2
│   ├── bowtie2-align-l
│   ├── bowtie2-align-l-debug
│   ├── bowtie2-align-s
│   ├── bowtie2-align-s-debug
│   ├── fastq-dump
│   ├── samtools
│   └── trimmomatic-0.39.jar
├── __init__.py
├── main.py
├── resource
│   ├── __init__.py
│   ├── logging.conf
│   ├── reference_config.json
│   ├── template_report.html
│   └── tool_config.json
└── utils
    ├── bam.py
    ├── config.py
    ├── fastq.py
    ├── __init__.py
    ├── logger.py
    ├── plot.py
    ├── report.py
    ├── sam.py
    ├── stat.py
    └── tag.py

Help

If you have any questions or require assistance using EVAtool, please contact us: xieguiyan@hust.edu.cn. More informations and usage could be found in the EVAtool web.