Add optional arguments to manually set alignment preset and alignment scoring-matrix

RIVM-bioinformatics / AmpliGone

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

https://rivm-bioinformatics.github.io/AmpliGone/

GNU Affero General Public License v3.0

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Add optional arguments to manually set alignment preset and alignment scoring-matrix #75

Closed florianzwagemaker closed 5 months ago

florianzwagemaker commented 10 months ago

This is considered a breaking-change as previously set default alignment scoring parameters are removed in favour of default-values determined by the aligner itself.

If you need specific scoring-matrixes for a certain pathogen (i.e. the analysis of RNA viruses often goes better with some adjusted scoring-parameters) then you can set and tune these scorings yourself now

sonarcloud[bot] commented 5 months ago

Quality Gate passed

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