I am new to using Airrflow, I was wondering if there is any plan/effort to integrate dandelion into the pipeline? https://github.com/zktuong/dandelion I was just wondering as I did not see any mention here nor on github.

Hi Paul, we are currently not planning to integrate dandelion into the pipeline. Is there any particular feature from dandelion that you are interested in?

I am learning still. But the pre-processing of dandelion seems to be working rather well. Although it seems similar to what airflow does, but I do get different results. So pre-processing in dandelion is essentially a post-processing of cellranger output.

it’s also possible to re-annotate the contigs with change-O, and airrflow does that by default (it can be deactivated with

--reassign false.

The main difference is that change-O starts processing with the filtered_contig_annotations.csv or AIRR_rearrangement.tsv file (we only support the latter in airrflow), whereas Dandelion recommends using the all_contig_annotations.csv. This is because they also process reads missing the V gene but with D and J genes using

blastn.