Update docs2

[priesgo]

• Update some of the figures in the documentation to higher resolution versions from the manuscript
• Include the system design diagram in the overview
• Describe better how to use a custom reference genome. Change BWA by BWA mem 2 and describe how to use SnpEff

Closes https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/issues/46 Closes https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/issues/47 Closes https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/issues/48

[codecov[bot]]

Codecov Report

Patch and project coverage have no change.

Comparison is base (04cb89b) 85.51% compared to head (121a329) 85.51%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #115 +/- ## ======================================== Coverage 85.51% 85.51% ======================================== Files 48 48 Lines 4924 4924 ======================================== Hits 4211 4211 Misses 713 713 ```

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