seqfu view

view is one of the core subprograms of SeqFu.

It can be used to visually inspect a FASTQ file printing colored bars for quality scores and highlighting oligonucleotide matches.

Usage: view [options] <inputfile> [<input_reverse>]

View a FASTA/FASTQ file for manual inspection, allowing to search for
an oligonucleotide.

Options:
  -o, --oligo1 OLIGO     Match oligo, with ambiguous IUPAC chars allowed
                         (rev. compl. search is performed), color blue
  -r, --oligo2 OLIGO     Second oligo to be scanned for, color red
  -q, --qual-scale STR   Quality thresholds, seven values
                         separated by columns [default: 3:15:25:28:30:35:40]

  --match-ths FLOAT      Oligo matching threshold [default: 0.75]
  --min-matches INT      Oligo minimum matches [default: 5]
  --max-mismatches INT   Oligo maxmimum mismataches [default: 2]
  --ascii                Use simple ASCII chars instead of UNICODE to
                         render the quality values
  -Q, --qual-chars       Show quality characters instead of bars
  -n, --nocolor          Disable colored output
  --verbose              Show extra information
  -h, --help             Show this help

Example output

The quality scores are rendered as colored bars (grey, red, yellow, green) of different heights. Matching oligos are rendered as blue arrows (forward) or red arrows (reverse).

Important hints

Disabling wordwrap

SeqFu view is designed for a manual inspection, and thus it's very convenient to pipe the output to less to avoid being misled by word-wraps:

seqfu view sequence.fq | less -SR

(in less: -S prevents word-wrap, and -R will preserve the colored output)

Encoding of "graphical" bars

The graphical rendering of the quality values is done using Unicode characters (UTF-8 encoding), thus requiring both the host system and the terminal emulator to support UTF-8. A simple test to check if your terminal supports Unicode is to type:

echo -e '\xe2\x82\xac'

If you see the Euro character (€) then your terminal fully supports UTF-8. If not, you can use --ascii or --qual-chars.

The following screenshot shows how quality scores are rendered using the different options:

• Default view with quality scale

• Graphical representation of the quality with ASCII characters

• Quality encoded as in the FASTQ file, but colored

Screenshot