Usage Instructions - StephenFordham/BacGenomePipeline GitHub Wiki

Usage Instructions

For useful usage instructions, run BacGenomePipline --help

BacGenomePipline can be run in one of four usage modes. The usage mode must be specified explicitly in the terminal. A selection of examples of BacGenomePipeline run in different usage modes is shown at the bottom of the help message and in the usage example section on this page.

usage: BacGenomePipeline (--pipeline | --pipe_red_mem | --assembly | --annotation)
--fastq_file READS
       --help --version
       [--nanostats] [--medaka_polish]
       [--mean_q_weight] [--asm_fasta]
       [--genome_size SIZE]  [--asm_coverage INT]
       [--flye_dir DIR_NAME] [--polished_dir DIR_NAME]
       [--amr_dir DIR_NAME]  [--vir_dir DIR_NAME]

Complete Bacterial Genome Assembly and Annotation Pipeline

optional arguments:
  -h, --help            show this help message and exit
  --pipeline            Runs the entire Pipeline
  --pipe_red_mem        Runs the entire Pipeline with reduced memory
                        consumption
  --assembly            Runs the assembly portion of the pipeline
  --annotation          Runs the annotation portion of the pipeline

Version:
  --version             Print version and exit.

Input fastq Reads (a fastq file is required):
  -f , --fastq_file     Specify an input Fastq file for the Pipeline and
                        assembly modes

Pipeline Options:
  -n, --nanostats       Optionally run NanoStats on your filtered read set
  -m, --medaka_polish   Optionally run NanoStats on your filtered read set
  -s , --asm_fasta      Add Genome assembly in fasta format
  -w , --q_weight       Add mean_q_weight for read filtering

Optional flye assembly arguments
(To reduce memory consumption for large genome assemblies):
  -g , --genome_size    Estimated genome size (for example, 5m or 2.6g)
  -c , --asm_coverage   reduced coverage for initial disjointig assembly [not
                        set]

Directory names:
  -d , --flye_dir       Specify a flye genome assembly directory name
  -p , --polished_dir   Specify a medaka polished genome directory name
  -a , --amr_dir        Specify a antimicrobial resistance directory name
  -v , --vir_dir        Specify a virulence gene directory name

Did you know? BacGenomePipeline can be run in modes

These modes include: pipeline, which runs the entire BacGenomePipeline workflow,
pipe_red_mem, which uses less memory by using use a subset of the longest reads 
for initial disjointig by specifying --asm-coverage and --genome-size options. 
The assembly mode runs assembly and polishing steps only. For this step, 
annotation is excluded. Finally the annotation mode takes a genome assembly and 
annotates it for antimicrobial and virulence genes 

Example Usage:
BacGenomePipeline --pipeline -f reads.fastq
BacGenomePipeline --pipeline -f reads.fastq.gz -m -n
BacGenomePipeline --pipe_red_mem -f reads.fastq -g 5.7m -c 40 -n -m
BacGenomePipeline --annotation -s assembly.fasta
BacGenomePipeline --assembly -f reads.fastq -n -m

Example Usage

BacGenomePipeline --pipeline -f reads.fastq
BacGenomePipeline --pipeline -f reads.fastq.gz -m -n
BacGenomePipeline --pipe_red_mem -f reads.fastq -g 5.7m -c 40 -n -m
BacGenomePipeline --annotation -s assembly.fasta
BacGenomePipeline --assembly -f reads.fastq -n -m