Run fastp

The fastp is a tool designed to provide ultrafast all-in-one preprocessing and quality control for FastQ data.

Usage

fastp(fq1, ofile1, ..., fq2 = NULL, ofile2 = NULL, fastp = NULL)

Arguments

fq1, fq2

A string of fastq file path.

ofile1, ofile2

A string of path to the output fastq file.

...

<dynamic dots> Additional arguments passed to fastp command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(fastp()).

fastp

A string of path to fastp command.

Value

A command object.

See also

• https://github.com/OpenGene/fastp

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: allele_counter(), bcftools(), bedtools(), bowtie2(), bwa(), cellranger(), conda(), fastq_pair(), gistic2(), kraken2(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()