Overview of mapping pipeline using Galaxy server, and generation of an expected allele match matrix. Our Galaxy-based mapping pipeline is shown for both class I (a) and DRB (b) sequence reads. The parsed “2 F” reads are used to limit the subset of subsequent alleles for matching since all named class I alleles have 2 F sequences as shown (c). The expected allele match matrix is shown for class I alleles (d). Type 1 matches are full, 100% identity matches along the entire read length. Type 0 are partial matches, where the read is longer than the reference allele (and contains novel sequence). Null matches (.) indicate no expected read match based on the lack of a reference allele sequence.
Lank et al. BMC Genomics 2012 13:378 doi:10.1186/1471-2164-13-378