Concepts

Interfaces

There are two major approaches to use GASiC. The first is the command line interface, the second is the scripting interface.

Command Line Interface

For the command line interface, GASiC provides three python scripts:

• run_mappers.py perfroms read alignment/mapping. The generated output is in a format readily usable by the following GASiC steps.
• create_matrix.py calculates the similarity matrix encoding the sequence similarities of the reference genomes.
• correct_abundances.py estimates the true abundances for all genomes in the dataset using the alignment information and the similarity matrix.

Scripting Interface

GASiCs scripting interface allows the user to create more versatile and powerful analysis scripts. This is useful, when tasks should be automated or a finer control of the single steps is required.

Instead of running the command line scripts one by one, all steps can be bundled in a single python script file. To this end, the user can import the corresponding modules and access the underlying functions directly.

• Read mapping: Wrappers for the read mapping tools are available in core/tools.py. Just do a from core import tools to get access to all implemented wrappers.
• Similarity Estimation: Do a import create_matrix to gain access to the fuctions for calculating the similarity matrix.
• Similarity Correction: Do a import correct_abundances to gain access to the fuctions for estimating the true abundances.

Wrapper

GASiC strongly relies on external software for read mapping and read simulation. Since GASiC should work with any mapping tool supporting the SAM format (http://samtools.sourceforge.net/), the user can decide which tool should be used.

GASiC already provides wrappers for the mapping tools bowtie, bowtie2, and BWA and for the read simulators Mason and dwgsim. More wrappers can be added easily by creating a simple wrapper function and adding this wrapper function to the corresponding wrapper list. Step by step instructions are given in the source code core/tools.py.