Pipeline for detection of potential AMG in assembled metagenome using BLASTP
This pipeline necessites two distinct BLASTP databases. One should contain bacterial proteins and another only viral proteins. The databases should be accompanied with a log containing Figfam ID present in the bacterial database and their annotations. Finaly a taxonomic log should provide taxonomic informations regarding the bacterial sequences present in the database. A pipeline to construct the bacterial database and necessary logs is available in https://github.com/aponsero/CreateDB-BLASTP-Patric .
ncbi-BLAST+ (at least version 2.3.0) should be previously installed and included in the user PATH.
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 .
please modify the
- SAMPLE = indicate here the metagenome file to analyze
- SAMPLE_DIR = indicate here the output directory
- BACTERIAL_DB = indicate here the BLASTP Bacterial file (.faa)
- VIRAL_DB = indicate here the BLASTP viral file (.faa)
- FIG_LOG = indicate here the FigFam log
- TAX_LOG = indicate here the taxonomic log
- 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".
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 ./submit.sh
Will place in queue two successive jobs for the analysis. The final output is located in $SAMPLE_DIR/results_AMG.log