My initial classification was:
- One gets raw data and maps it to VDJ
- One assembles mapped reads into clonotypes/clones
- One analyzes the list of clones (the software packages should not necessary work with raw data)
I think it can be wise to merge
- List of B cell clonal identification software
- List of V(D)J mapping software that works with complex datasets
into a single page with a table, but I recall that some RNA-Seq/single cell RNA-Seq software are not very optimized for conventional amplicon libraries. I’ll think of the table design and post it here, please give your suggestions on what columns/parameters we need to include in it.