fastqc

This function is used for fastq file quality control.

Note

This function is calling FASTQC.

FASTQC official docs

Andrews, Simon. “FastQC: a quality control tool for high throughput sequence data.” (2010).

Parameters

fastqc(fastqInput=None, fastqcOutputDir=None,
       threads=1, other_params=None, stepNum=None,
       upstream=None, verbose=True)

  • fastqInput: list, fastq files.

  • fastqcOutputDir: str, output result folder, None means the same folder as input files.

  • threads: int, how many thread to use.

  • other_params: dict, other parameters passing to FASTQC.

    “-parameter”: True means “-parameter” in command line. “-parameter”: 1 means “-parameter 1” in command line.

  • stepNum: int or str, step flag for folder name.

  • upstream: upstream output results, used for pipeline.

  • verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

Example usage:

fq1 = ["test1_1.fq", "test2_1.fq"]

fastqc(fastqInput=fq1)