Hi everyone! I’m working with a plasmid-based library in which each insert contains VH–(linker)–VL in a single fragment. Our sequencing reads often capture both heavy and light variable regions and i’ve been trying to fabricate mock data to test if the sequencing will work in an airrflow protocol. Without success. Does anyone know if airflow would crash if it can’t find diversity of constant regions or requires to have multiple clones of different germlines to clear steps in the pipeline?. Anyone has experience generating mock data? I’ve tried multiple ways for adapting the pipeline to accommodate scFv constructs where both chains are in one read.

Hi Christian, what you are describing seems to be a very specific protocol and it will definitely not work with airrflow. Airrflow assumes that a read contains either VH or VL chains. That said you could try if using the presto tool of the Immcantation framework you can preprocess the reads to have separate VH and VL and then you could potentially save the sequences in fasta format and use airflow downstream with the assembled mode.