quality

This module handles everything about quality analysis.

quality.discardHighError(sras)

Reads the quality analysis made by Qualimap and discards the runs that yielded a low quality alignment.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

Returns:

list: List of filtered tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

quality.runFastQC(sras)

Runs a quality analysis on the reads using FastQC.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

quality.runQualimap(sras)

Runs a quality analysis on the alignments using Qualimap.

It analyzes the quality of the alignment of each run against each viral genome.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID