Pipeline that generates amplicon sequencing data using BioGrinder

Features of the pipeline

- Generating rRNA amplicon sequencing data using BioGrinder
- Adding a start and end primer to the given target database
- Combining output files of BioGrinder amplicons sequencing data to one file containing forward amplicons and one file containing reverse amplicons

Running the Pipeline

- Pull the main branch from github
- Install the needed dependencies
- Make sure a file contanining a 16S/18S database is present in the /data/database directory
- Make sure a file containing the primers is present the /data/primers directory
- run the BioGrinder.sh with the correct parameters(described bellow)
- Ouput directory will be created in the output folder

Parameters

- Mandatory parameters:
    - "-d (Database name)" Use this paraemter to give the name of the database that will be used. 
        - Mandatory.
    - "-n (Name for the run)" Use this parameter to give a name to the pipeline run.
        - Mandatory.
- Change default values:
    - "-r (Amplicon length)" Use this parameter to change the read length. 
        - Default is 151.
    - "-p (Primer file)" Use this parameter to change the name of the primer file that will be used.
        - Default is RC-PCR-primers-changed.fasta.
- Optional parameters:
    - "-x" Add this paramameter to add the first forward and last reverse primer to you target database.
        - Optional.
    - "-a (abundence file name)" This parameters enables to specify the relative abundance of the reference sequences manually in an input file.
        - Optional.

Development

- For development follow the following steps:
    - Pull the main branch
    - Make sure all the dependencies are installed
- For testing during development:
    - Add a fasta file contanining a 16S/18S database in the /data/database directory
    - Add a fasta file containing the primers in the /data/primers directory
    - Run the BioGrinder.sh script with the correct parameters(described above)

Dependencies

- BioGrinder
- UNIX based system