Package: evatool
EVAtoolQuick startIf you would like to get start using EVAtool, please following the any of the follwing document.Quick start from  PyPIQuick start from DockerIntroductionEVAtool (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 inPython >=3.5,JupyterandHTML.Table of ContentsSystem RequirementsPythonInstallation with pipInstallation from sourceQuick Start by pipDockerInstallationQuick Start by dockerAdvanced optionDirectory treeHelpSystem RequirementsWindows (>= 7), Mac OS X (>= 10.8) or LinuxPython >= 3.5JDK 8All other software dependencies are installed automatically when installing EVAtool. Some softwares versions are as follows:samtools = 1.12bowtie2 = 2.4.2fastq-dump = 2.10.9trimmomatic-0.39.jarbedtools = 2.30.0PythonInstallation withpipThe Python version of EVAtool can be installed by running the following from a terminal:pip install EVAtoolInstallation of EVAtool and all dependencies should take no more than one minutes.Installation from sourceThe 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 --userQuick Start by pipTo begin, the human genome and seven types references needed to be download fromhttp://bioinfo.life.hust.edu.cn/EVAtool/ref/refs.zipand 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.zipIf 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.fastqandexample.fastq.gz.DockerInstallationThe docker image of evatool can be accessed by running the following from a terminal:docker pull guobioinfolab/evatoolThen, prepare reference data and sequence data like thepippart: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 dockerTake the example.fastq.gz as example:docker run -it -v $PWD:/work_path -w /work_path guobioinfolab/evatool -i example.fastq.gz -o .Advanced optionCustom ncRNA type(s)Based on existing reference sequenceschange 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 sequencesThree steps :Add the ncRNA reference and index into refs;mkdir [ncRNA name]
add the reference and index to the directoryChange the input parameter of ncRNA type list;-n  "miRNA" "rRNA" "tRNA"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.pyHelpIf you have any questions or require assistance using EVAtool, please contact us:xieguiyan@hust.edu.cn. More informations and usage could be found in theEVAtool web.