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The cutadapt usage says that output can be written to a file using the -o option

    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

But the brackets around [-o output.fastq] suggest this is optional. Reading a bit further we see:

... Without the -o option, output is sent to standard output.

This suggests output can be specified in 2 ways:

• to a file, using the -o option
  • cutadapt -a CGTAATTCGCG -o trimmed.fastq  small.fq
• to standard output without the -o option
  • cutadapt -a CGTAATTCGCG small.fq > 1> trimmed.fastq

The cutadapt usage says an input.fastq file is a required argument:

    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

But again, reading a bit further we see:

Input may also be in FASTA format. ...                           Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.


This suggests input can be specified in 2 ways:

• from a file, using the -o option
  • cutadapt -a CGTAATTCGCG -o trimmed.fastq  fastq  small.fq
• from standard input if the input.fastq argument is replaced with a dash ( - )
  
  • cat small.fq | cutadapt -a CGTAATTCGCG -o trimmed.fastq  fastq  -
    

And also says that the input.fastq file can be provided in one of three compression formats.