# Basecalling process carried out by full_1dsq_basecaller.py/.exe

I am unable to understand what exactly the full_1dsq_basecaller.py/.exe script does. Is it giving the consensus sequence for linear and complementary strand, or it is just giving the reads that came from the complimentary strand?

If we are getting two fastq files as output which one we should use for alignment?

Thank you in advance. I greatly appreciate any help

My understanding is that the 1D$^2$ process is carried out in three stages:
Because the linking is not a physical link, it's not a good idea to use 1D$^2$ for amplicon reads; the likelihood of two complementary reads from different templates appearing one after another is too high.