Virus Identification On Site

[TOC]

• Java 1.8

• Python 2.7

• Perl 5

• Python 3rd libraries

  xlwt xlrd biopython numpy ReportLab matplotlib django1.11.3 django_extensions

There are mainly three steps, including short reads' mapping with Bowtie2, assembling with Velvet, contigs' mapping with blast+. Deloy the bioinformatics softwares , and add the commond to PATH.

• CD-HIT
• Bowtie2
• velvet
• BLAST+

adenovirus two samples: -jiayan -liublood

You need to upload the raw datas, after uploading the files were in the directory of "$PATH/VIOS/media/2018/02/raw_datas/". You can get the them from BaiduYun_demoData.

BEFORE, set the DATABASE_HOME in your environment variables.

export DATABASE_HOME=$YOUR_PATH/database
##genome directory
$DATABASE_HOME/genomes
##virus gene/genome directory
$DATABASE_HOME/blastDB

1. genome

   Go to the modul 用户自有参考数据库索引 on the web. Then , You can search species genome from UCSC to get host "genome name" you wanna map aginst to remove the host genetics informations from the raw data reads. And, name the "genome name" with the readable name in the "host name" on the web.

   For example, you can add "hg38" and "human" in the input box attached a label with "genome name" and "host name", respectively.

   There are also some common species

   • model animal in the lab

   • poultry and livestock

   • primates (closer to human relations)

     genome name	host name
     hg38	human
     mm10	house_mouse
     rn6	Norway_rat
     galGal5	chicken
     felCat8	cat
     susScr3	pig
     oryCun2	rabbit
     oviAri3	sheep
     bosTau8	cow
     equCab2	horse
     myoLuc2	microbat
     papAnu2	baboon
     panTro5	chimpanzee
     gorGor5	gorilla
     rheMac8	rhesus_monkey

2. virus gene/genome

   • Step1. pre-handle the virus database referring to the paper;
   • Step2. name it with "nt_viruses_final.fasta";
   • Step3. put the file into the $DATABASE_HOME/blastDB/nt_viruses/final directory;
   • Step4. Go to the the modelue 用户自有参考数据库索引, press the "Update Viruses" button.

   Besides, you can also custom the virus 's some family like Filoviridae which Ebola belongs to. The process method is like the virus handling method above, in addition, modify the variables(nt_viruses_family_name_list,nt_viruses_family_name_readable_list) in the /VIOS/ngs/scripts/config_paras.py script.

   Well, you can email at Su Yanan [email protected] to get the virus database, I'll share with you through cloud storage. You can download nt_viruses_final database from BaiduYun_database.

• Step1. Config MYSQL database

  $apt install mysql-server mysql-client libmysqlclient-dev  #REMEMBER ROOT PASSWORD
  $myslq -u root -p
  mysql>CREATE DATABSAE vios_db;
  mysql>USE vios_db;
  

  Besides, you can change MySQL to other database like Postgres.

• Step2. Clone the VIOS project code locally

  #clone the VIOS codes locally:
  git clone git:https://github.com/suyanan/VIOS.git
  
  #Modify the /VIOS/VIOS/settings.py file
  ##replace those variables:USER/PASSWORD
  DATABASES = {
      'default': {
          'ENGINE': 'django.db.backends.mysql',
          'NAME': 'vios_db',
          'HOST':'127.0.0.1',
          'PORT':'3306',
          'USER':'root',
          'PASSWORD':'1234aaaa',
      }
  }
  ##ADD your IP
  ALLOWED_HOSTS = [
      u'127.0.0.1',
      u'localhost',
      u'your PC IP',
  ]
  

• Step3. start the VIOS project

  $python /VIOS/manage.py runserver 0.0.0.0:8000
  
  #apply the migrations for VIOS
  $python manage.py migrate
  

  Open the VIOS_dress with link 127.0.0.1:8000

• Step4. ANALYSIS: database

• Step5. ANALYSIS: pipeline

• Step6. ANALYSIS: visualization

2018.02.09

The End