Reconstruction of germline sequences from alignment data

The tool takes the individual segment alignment information for each sequence and reconstructs a full length germline sequence from the V(D)J reference sequences.

To reconstruct the germline, trims V(D)J germline segments and N/P regions by alignment length and concatenates them together. It puts Ns in the untemplated N/P regions and optionally masks the D with Ns (-g dmask). also looks for and corrects cases where the alignment tool assigned the same part of the input sequence to two different regions (eg, assigning the same nucleotides to N/P and J).

At the end of the germline reconstruction process, each sequence has been assigned a germline specific to the sequence.

When the (--cloned) flag is specified, the process is the same except it is clone specific and results in the creation of one germline per clone. selects first a single V and J allele to use as the germline from all the assigned annotations in each clone. The selection is made by simple majority rule of all the allele calls in the clone. After the germline reconstruction process, all sequences belonging to the same clone have been assigned the same germline.