Metadata-Version: 1.1
Name: BacGenomePipeline
Version: 1.0.9
Summary: Complete Bacterial Genome Assembly and Annotation Pipeline
Home-page: https://github.com/StephenFordham/BacGenomePipeline
Author: Stephen Fordham
Author-email: sfstephenfordham@gmail.com
License: MIT
Description: BacGenomePipeline
        
        Complete Bacterial Genome Assembly and Annotation Pipeline
        
        Program developed by Stephen Fordham
        
        
        General Description
        
        BacGenomePipeline is a complete convenience bacterial genome assembly pipeline. Assembled and annotated bacterial
        genomes can be created with only raw reads as input! BacGenomePipeline can accept either fastq or gzipped fastq files.
        Relax and grab a coffee while BacGenomePipeline does the genomic heavy lifting.
        
        
        This pipeline filters raw reads to produce the best 500mb reads.
        The filtering process also places weight on read quality, to ensure small high quality reads are not discarded.
        This is considered vital to aid the recovery of small plasmids present within bacterial strains.
        
        
        Optionally, the user can run Nanostat to assess read quality metrics. The best reads are then assembled using the
        flye genome assembler with settings adjusted to help recovery of plasmids with an imbalanced distribution.
        Optionally, the assembly is then polished with one round of medaka-consensus polishing. The polished assembly is annotated 
        using staramr which scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases
        (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and abricate and 
        compiles a summary report of detected antimicrobial resistance and virulence genes.
        
        Additionally, BacGenomePipeline can be run in 4 modes. 
        
        These modes include:
         Running the entire pipeline workflow
            --pipeline
         Running the pipeline using reduced memory by setting parameters for genome size and coverage for initial disjointings
            --pipe_red_mem
         Running a genome only assembly
            --assembly
         Running the annotation step on an pre-exisiing genome assembly in FASTA format.
            --annotation   
            
               
        For usage instructions, run:
        
            BacGenomePipeline --help
        
        Currently BacGenomePipeline has been tested and runs on Linux OS.
        
        To run BacGenomePipeline, you must also install the following programs by running the following commands:
        
            conda install -c bioconda filtlong==0.2.0
        
            conda install -c bioconda flye==2.8.1
            
            conda install -c bioconda abricate==1.0.1
        
        
        
        
        
        
        Change Log
        ==========
        
        BacGenomePipeline
        
        v.1.0.9 (20/02/21)
        -------------------
        
        - BacGenomePipeline Usage instructions update
        - virulence gene detection added
        - pipeline option modes added 
        
Keywords: Genome Assembly,WGS,bacterial pipeline,prokaryotic,bacterial genome assembly
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Education
Classifier: Operating System :: POSIX :: Linux
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
