seqfu head

head is one of the core subprograms of SeqFu.

It will print the first sequences of a FASTX file (like GNU head), but can be instructed to skip a number of sequences between each printed one.

Usage: head [options] [<inputfile> ...]

Select a number of sequences from the beginning of a file, allowing
to select a fraction of the reads (for example to print 100 reads,
selecting one every 10).

  -n, --num NUM          Print the first NUM sequences [default: 10]
  -k, --skip SKIP        Print one sequence every SKIP [default: 0]
  -p, --prefix STRING    Rename sequences with prefix + incremental number
  -s, --strip-comments   Remove comments
  -b, --basename         prepend basename to sequence name
  -v, --verbose          Verbose output
  --quiet                Don't print warnings
  --help                 Show this help

  --fasta                Force FASTA output
  --fastq                Force FASTQ output
  --sep STRING           Sequence name fields separator [default: _]
  -q, --fastq-qual INT   FASTQ default quality [default: 33]```


By default the program prints the first 10 sequences of a file (the number can be changed with -n or --num).

Sometimes to have a preview of a file we can add the --skip (or -k for short) parameter to take a sequence every N.

The following examples shows the output of seqfu head -n 10, and seqfu head -n 5 -k 4):


Input and output

seqfu head takes as input one ore more FASTA/FASTQ files (or reads from the standard input if no filenames are provided, or - is added to the list). The output will be in the same format as the input, unless --fasta or --fastq are specified to force a different output.


Screenshot of