What does mccortex build do if it encounters Ns in the read?

[yeban]

Are k-mers containing N automatically ignored?

[noporpoise]

Yes, sequences are broken up at N bases.

For example, the input AACNNCTA gives kmers AAC and CTA:

$ bin/mccortex31 build -q -k 3 --sample Test --seq <(echo 'AACNNCTA') - | bin/mccortex31 view -q --kmers -
AAC 1 ........
CTA 1 ........

[yeban]

Thanks.