[[alignments]]
Alignments
~~~~~~~~~~

[[algorithm]]
Algorithm
^^^^^^^^^

Performs Smith-Waterman alignments of the genomic templates. Using a
slight alteration of the Smith-Waterman score matrix, we enforce that V
can only be deleted on the 3' side and J on the 5' side (thus enforcing
the alignment on the other side until the end of the read or of the
genomic template). D is aligned using a classical Smith-Waterman local
alignment approach allowing gene deletions on both sides.

include::alignment_commands.adoc[]

include::alignments_output.adoc[]
