identifyAdapter

This function is used for detecting adapters in paired end fastq files.

Note

This function is calling AdapterRemoval. This function is only suit for paired data.

adapterremoval official docs

Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. “AdapterRemoval v2: rapid adapter trimming, identification, and read merging.” BMC research notes 9.1 (2016): 1-7.

Parameters

identifyAdapter(fqInput1=None, fqInput2=None,
                outputdir=None, threads=1,
                other_params=None, stepNum=None,
                upstream=None, verbose=True)

  • fqInput1: list, fastq 1 files.

  • fqInput2: list, fastq 2 files.

  • outputdir: 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 command “AdapterRemoval –identify-adapters”.

    “-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"]
fq2 = ["test1_2.fq", "test2_2.fq"]

identifyAdapter(fqInput1=fq1, fqInput2=fq2)