Paired end 150?

[rafischulman]

Hi,

I just read your paper introducing this tool- very well done!

I'm getting set up to run COJAC myself on our own data. The amplicon was generated with the ARTIC 3 method, so we should be set on that front. However, sequencing was paired end 150, rather than 250. I know that this will create some gaps within reads, but am still curious to see how this algorithm performs. Are there any settings I will need to adjust to make COJAC run on our data?

Thanks