Alignment mode

The mapper supports two different modes of alignment: local (default) and global.

The alignment mode is set using the -a/--alignmode parameter.

In local mode, -a local, alignments are chosen to be locally optimal, i.e. the mapper looks for the highest scoring alignment of part of the read. That is, unaligned ends are not penalized in any way.

In global mode4.2, -a global, the mapper is forced to look for the highest scoring alignment of the entire read. That is, unaligned ends are no longer free.

Generally, we recommend that you stick to local alignment, as there are several reasons, why you may not want to force the ends of a raw read sequence to align:

  1. Read quality deteriorates towards the end of a read, so you may end up aligning noise.
  2. If present, untrimmed adapter sequence cannot be aligned in any meaningful way.
  3. Structural variation may be present in the sample, so the reference may not have corresponding sequence for all of the read.
In general, unaligned ends express a lack of confidence in a portion of the read; information that can be very helpful for several, common downstream analyses.


Footnotes

... mode4.2
This is sometimes called semi-global alignment, because the alignment is global with respect to the read, but remains local with respect to the reference.