[[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.

WARNING: Alignments represent a critical step for a precise probabilistic 
characterization of your sequences. Make sure you use all the information you 
have on your sequences (e.g use the knowledge of your primers positions to 
provide template specific alignment offsets) for optimal result. 

include::alignment_commands.adoc[]

include::alignments_output.adoc[]
