Maybe the following is helpful for some of you:
SciReptor - our group’s single-cell Ig analysis toolkit - ships with a manually curated C57BL/6J Ig germline database (DB). This DB is based on the NCBI mouse genome assemblies 37 and 38 [1] and has been extensively cross-checked for accurate segment boundaries using single-cell transcript data. It uses the IgBLAST/NCBI segment nomenclature, which refers to Johnston et al. and Brekke et al… We have now released a new version of this library.
The data is now provided as CSVs containing the start-end positions of the segments [2] relative to the NCBIm38 assembly. We hope that by using this format the DB versioning will become more simple and transparent compared to raw FASTA files.
[1] The NCBIm38 assembly is now called GRCm38 by Ensembl, but the segment locations are still identical. We will change the designation in the next release.
[2] For V segments, only the positions of exon 2 are provided since exon 1 always encodes the leader peptide. Exon 1 positions are available if the exon is productive.