Paper: Changes/suggations on affiliations/acknowledgements/summary

[jfy133]

Some further comments below, I still need to make suggestions on the statement of need

My read-through notes:

• [ ] Affiliations: Doesn't Sofia have 3?
• [x] Summary: isn't necessarily correct: can be eukaruotes (not micrbes),
• [x] Summary: first sentence is history that doesn't necessarily prime the main question
• [x] Summary: Missing wrap up sentence
• [x] SoN: Wrong citation MEGAN/MALT
• [ ] SoN: maybe shortly describe example problem of varying profiler output formats
• [ ] SoN: Condense other tools sentences into one pargraph, mention kraken2tools(?), QIIME2 is mostly aimed at 16S etc, doesn't CAMI challenge also have a sort of format (more generic)?
• [ ] SoN: Missing caveats (which it does/doesn't do, e.g. doesn't do analysis, fixed output to read counts)
• [x] Acknolwegments: Max Planck Society
• [x] Acknowedgments: RAPID-Seq should have quotes

Questions:

• [ ] TAXPASTA or taxpasta or Taxpasta? Should pick one and use everywhere (e.g. docs has TAXPASTA, taxpasta, Taxpasta)
• [ ] Do we care/want a simple image summarising the tool, like a graphical summary/figure?

[jfy133]

Shower thoughts:

• [ ] should explicitly mention normally researchers would have to write their own parsers for each and every of the tools
• even biom format would require data parting to get it into the right format, AFAICR it didn't have parses for different tools
• [ ] Krakentools only works for a specific 'family' of profilers (kraken and derivatives)