SMRT Pipe modules and their parameters - pb-dyim/SMRT-Analysis GitHub Wiki

Following is an overview of some of the common modules included in SMRT Pipe and their parameters. Not all modules or parameters are listed here.

Developers interested in even finer control should look inside the validateSettings method for each python analysis module. By convention, all of the settings known to the analysis module are referenced in this method.

Global Parameters

Global parameters are potentially used in multiple modules. In the SMRT Pipe internals, they are accessed in the “global” namespace. Following are some common global parameters:

reference
  • Specifies the name of a reference repository entry or FASTA file for mapping reads. Required for resequencing workflows.
  • Default value: None
control
  • Specifies the name of a reference repository entry or FASTA file for mapping spike-in control reads. Optional
  • Default value: None
use_subreads
  • Specifies whether to divide reads into subreads using the adapter region boundaries found by the primary analysis software. Optional
  • Default value: True
num_stats_regions
  • Specifies how many regions to use when reporting region statistics such as depth of coverage and variant density. Optional
  • Default value: 500

Modules