[ALPHABET, DOC] Improve documentation of the quality alphabets

[smehringer]

Description

Should be tackled after the new alphabet #267 is included!

The quality alphabets are not understood easily. Should I use phred42 pr phred63? What's the difference? And which "Format" (regarding the Sanger/Illumina/Solexa encoding) is used?

Our documentation is not completely clear about this and should be improved.

References:

• Wikipedia on phred scores: https://en.wikipedia.org/wiki/FASTQ_format#Quality
• Our documentation on the quality landing page
• Hannes Dissertation (see issue comment here for an excerpt)
• [EDIT (irallia)] Explanation about Phred+33 and Phred+64 http://people.duke.edu/~ccc14/duke-hts-2018/bioinformatics/quality_scores.html#Phred-Encodings

Tasks

• Work yourself into what the phred alphabet is representing. First by reading our documentation, s.t. you have hands-on experience which parts are confusing.
• Improve the documentation on the quality landing page s.t. it is clearer to users what quality alphabet they should use in which case. Kind of a guide to follow.
• Also reference (\ref) the landing page documentation on the individual quality alphabets (phred42/63/68legacy) documentation, s.t. the user is pointed to the detailed documentation
• [EDIT (irallia)] Add a tutorial Phred score part to the alphabet tutorial. Add a snippet which represents a dna phred score combination to show the context for phred scores.
• [EDIT (irallia)] Give also an explanation about Phred+33 and Phred+64 (we use only Phred+33?)?