adapterremoval

This function is used for removing adapters in fastq files.

Note

This function is calling AdapterRemoval.

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

adapterremoval(fqInput1=None, fqInput2=None, outputdir=None,
               threads=1, paired=True,
               adapter1=["AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"],
               adapter2=["AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"],
               other_params={"--qualitybase": 33, "--gzip": True},
               stepNum=None, upstream=None, verbose=True)

  • fqInput1: list, fastq 1 files or single end files.

  • fqInput2: list, fastq 2 files or None for single end data.

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

  • threads: int, how many thread to use.

  • paired: boolean, paired end or single end.

  • adapter1: list, adapters for corresponding fqInput1.

  • adapter2: list, adapters for corresponding fqInput2, None for single end data.

  • other_params: dict, other parameters passing to command “AdapterRemoval”. “-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"]

adapterremoval(fqInput1=fq1, fqInput2=fq2, paired=True)