Output QC

[hoelzer]

I think currently there is no quality check of the generated consensuses?

I suggest having at least some simple qc e.g.

• check for the number of N
• pairwise sequence identity to e.g. the Wuhan reference sequence

to automatically decide which samples yield good enough consensus sequences for further processing.

We could even simply implement a python script that people are working on right now: https://gitlab.com/RKIBioinformaticsPipelines/president

Here, an input FASTA sequence is aligned to the Wuhan reference strain an a pairwise identity is calculated and reported in a tabular format.

[replikation]

agree we can sort the output a bit based on the alignment (wuhan is included here: https://github.com/replikation/poreCov/tree/master/data/reference_nCov19)