MG-Digger

A pipeline to search interest sequences in metagenomes.


Absolute Requirements :
- python 2.7.x 32 bits (x86)(https://www.python.org/downloads/)
- biopython (http://biopython.org/wiki/Download)
- blast >= 2.2.30 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/)


Keep Folder "NCBI_db" or move it and modify the path in the config file

For Windows:
- Don't forget to change your path (report documentation of Python: https://docs.python.org/2/using/index.html) 
  or (http://pythoncentral.io/add-python-to-path-python-is-not-recognized-as-an-internal-or-external-command/)

Important:
Metagenome with blank spaces in identifier sequences doesn't work, please use the cleaner option of MG-Digger to correct before analysis. 


########################################################### Graphical users interface ################################################################
MG-Digger GUI instructions:

First time:
- Run in command line python MG-Digger_gui.py'
- Click Edition > Set path (to configure the absolute paths of the blast databases folder and SRAToolkit if you want to move it)

If you don't have nr/nt local databases, and taxonomy databases or if you want to update databases:
- Click Edition > Update databases

To clean or convert a metagenome (fasta, fastq or SRA):
- Click Option > Metagenome cleaning

Usage:
- Choose your metagenome file and a reference fasta file.
- Select the group you want to study.
- Select BLAST method.
- Enter an e-value cut-off.
- Enter an e-mail to receive an e-mail when MG-Digger analysis will finish.
- Choose the number of CPUs you want to use for BLAST (Multiprocessing)
- Click "Run"

If you want limit the final result of metagenomic search, you can write in the good file in 'NCBI_folder', a list of nucleotide and protein GI number of species available in NCBI website line per line. 

############################################################### Command line #########################################################################
MG-Digger command line instructions:

First time:
- edit "config.py" file path to configure the absolute path of the blast database folder if you want to move the folder.

If you don't have nr/nt local database, and taxonomy database or you want to update database
- Run in command line 'python MG-Digger_cl.py -u'

If you want limit the final result of metagenomic search, you can write in the good file in 'NCBI_db' folder, a list of nucleeotide and protein GI number of species available in NCBI website line per line.

To clean or convert a metagenome (fasta, fastq or SRA):
- Run in command line 'python MG-Digger_cl.py -cleaner -m YOUR_METAGENOME

NAME
  MG-Digger_cl.py

VERSION
  1.00

CATEGORY
  Metagenomes; Bioinformatics

AUTHOR
  Jonathan VERNEAU <jonathan8313@gmail.com>

DESCRIPTION
  A pipeline to search interest sequences in metagenomes

usage: MG-Digger_cl.py [-v] [-h] [-p #] [-m #] [-i #] [-g #] [-e #] [-c #]
                     [-mail #] [-u] [-cleaner] [-min #] [-n #]

optional arguments:
  -v, --version         Show program's version number and exit
  -h, --help            Show this help message and exit
  -p #, --program #     Type of extraction ('16S', 'tblastn', 'blastx' or 'blastn')
  -m #, --metagenome #  path to the metagenome file
  -i #, --item #        path to the item file
  -g #, --group #       Group study ('All','Viruses','Archeae','Bacteria','Eukaryota','Megavirales')
  -e #, --evalue #      E-value
  -c #, --cpus #        Number of CPUs to use
  -mail #               Enter an e-mail address
  -u, --update          Update NCBI databases
  -cleaner, --cleaner   Clean metagenome
  -min #, --minus #     Minimum length per read (for metagenome cleaning)
  -n #, --maximum #     Maximum percent of n per read (for metagenome cleaning)

###########################################################################################################################################################

Citation

    MG-Digger: an automated pipeline to search for giant virus-related sequences in metagenomes. Front. Microbiol. - Virology (2016).

