bowtie2

This function is used for mapping WGS data.

Note

This function is calling bowtie2.

bowtie2 official docs

Langmead, Ben, and Steven L. Salzberg. “Fast gapped-read alignment with Bowtie 2.” Nature methods 9.4 (2012): 357.

Parameters

bowtie2(seqInput1=None, seqInput2=None, ref=None,
        outputdir=None, threads=1, paired=True,
        other_params={"-q": True, "-N": 1, "--time": True},
        stepNum=None, upstream=None,)

  • seqInput1: list, input _1 fastq files.

  • seqInput2: list, input _2 fastq files, None for single end.

  • ref: bowtie2 reference path.

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

  • threads: int, how many thread to use.

  • paired: True for paired data, False for single end data.

  • other_params: dict, other parameters passing to Bismark.

    “-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. This parameter can be True, which means a new pipeline start.

  • 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"]

bowtie2(seqInput1=fq1, seqInput2=fq2,
        ref="path_to_bowtie2_genome",
        threads=30, paired=True)