missing bases in low-covered homopolymer stretches

[hoelzer]

In regions with lower ONT read coverage single bases might be missed in the generated consensus due to issues in basecalling homopolymer stretches.

For example (position 11075, end of ORF1):

Maybe this can be fixed by additionally checking for deletions after Medaka that are in homopolymer (e.g. length > 6 nt) stretches and by again comparing to a reference (Wuhan) sequence. However, can be difficult if real deletions occur in homopolymers.

Maybe it's already fixed in the current ARTIC pipeline.

[hoelzer]

This issue for this specific location is also discussed (but not solved) here: https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473/14

[replikation]

• closing this, as its tagged as documentation