Metadata-Version: 2.1
Name: ProkaryoteAssembly
Version: 0.0.5
Summary: Internal BFSSI package for assembling prokaryotic genomes from short reads
Home-page: https://github.com/bfssi-forest-dussault/ProkaryoteAssembly
Author: Forest Dussault
Author-email: forest.dussault@canada.ca
License: UNKNOWN
Description: # ProkaryoteAssembly
        
        Two simple scripts to assemble prokaryotic genomes using paired-end reads.
        
        ## Pipeline Overview
        1. QC on reads with bbduk.sh (adapter trimming/quality filtering)
        2. Error-correction of reads with tadpole.sh
        3. Assembly of reads with skesa
        4. Alignment of error-corrected reads against draft assembly with bbmap.sh
        5. Polishing of assembly with pilon
        
        
        ## Usage
        The first script, `prokaryote_assemble.py`, operates on a single sample at a time.
        
        ```bash
        Usage: prokaryote_assemble.py [OPTIONS]
        
        Options:
          -1, --fwd_reads PATH  Path to forward reads (R1).  [required]
          -2, --rev_reads PATH  Path to reverse reads (R2).  [required]
          -o, --out_dir PATH    Root directory to store all output files.  [required]
          --version             Specify this flag to print the version and exit.
          --help                Show this message and exit.
        ```
        
        The second script, `prokaryote_assemble_dir.py`, will detect all *.fastq.gz files in
        a directory and run the assembly pipeline on each sample it can pair.
        
        ```bash
        Usage: prokaryote_assemble_dir.py [OPTIONS]
        
        Options:
          -i, --input_dir PATH  Directory containing all *.fastq.gz files to assemble.
                                [required]
          -o, --out_dir PATH    Root directory to store all output files.  [required]
          -f, --fwd_id TEXT     Pattern to detect forward reads. Defaults to "_R1".
          -r, --rev_id TEXT     Pattern to detect reverse reads. Defaults to "_R2".
          --help                Show this message and exit.
        
        ```
        
        ## Python (3.6) Dependencies
        - click
        
        ## External Dependencies
        **NOTE:** All external dependencies must be available via PATH.
        
        *Versions confirmed to work are in brackets.*
        - [skesa](https://github.com/ncbi/SKESA) (SKESA v.2.1-SVN_551987:557549M)
        - [BBMap](https://sourceforge.net/projects/bbmap/) (BBMap version 38.22)
        - [pilon](https://github.com/broadinstitute/pilon/wiki) (Pilon version 1.22)
        - [samtools](http://www.htslib.org/download/) (samtools 1.8 using htslib 1.8)
Platform: UNKNOWN
Description-Content-Type: text/markdown
