aponsero / UPROC_AMG_detection

Pipeline for detection of potential AMG in assembled metagenome using UPROC

UPROC_AMG_detection

Pipeline for detection of potential AMG in assembled metagenome using UPROC

Requirements

UPROC databases

This pipeline necessites to download a Uproc database and working model. Several databases are available in the Uproc homepage and Uproc provide a pipeline to create custom databases.

UPROC

Uproc (at least version 1.2.0) should be previously installed and included in the user PATH. Uproc is available at https://github.com/gobics/uproc.

Prodigal

Prodigal (at least version 2.6) should be installed. The location of installation should be provided in the config file. Prodigal is available at https://github.com/hyattpd/Prodigal .

Quick start

Edit scripts/config.sh file

please modify the

• SAMPLE = indicate here the metagenome file to analyze
• SAMPLE_DIR = indicate here the output directory
• DB_DIR = indicate here the Uproc database directory
• MODEL = indicate here the Uproc model directory
• PFAM_VIR = provide a list of known viral pfam id
• MAIL_USER = indicate here your arizona.edu email
• GROUP = indicate here your group affiliation

You can also modify

• BIN = change for your own bin directory.
• PRODIGAL = give the prodigal install folder.
• MAIL_TYPE = change the mail type option. By default set to "bea".
• QUEUE = change the submission queue. By default set to "standard".

Split input file

Run

./split.sh

This command will remove short contigs from the dataset (<500pb) and split the remaining contigs in manageable files for the analysis (10.000 contigs/files). The split files are stored in $SAMPLE_DIR/div/raw.

Once the job is completed successfully, the analysis can be run.

Run analysis

Run

./submit.sh

Will place in queue two successive jobs for the analysis. The final output is located in $SAMPLE_DIR/results_AMG.log