Novoalign with softclipping OFF (-o FullNW)?

[oiiio]

In the latest versions of novoalign, there is some softclipping for local alignment included by default. Supposedly this can be deactivated by using the parameters

-o FullNW

I have been trying to run novoalign with the following command line, in order to deactivate the softclipping:

novoalign -o SAM -o FullNW -d ref.ndx -f fastq1 fastq2 > file.sam

The above command runs fine and returns absolutely no errors. BUT, I feel like it is extremely suspicious that the run time is EQUAL regardless of -o FullNW for the same fastq files.

If you are turning off the local alignment step, shouldn't the mapping take much less time?

I am still new to NGS, and it probably shows

[sparks]

In the latest versions of novoalign, there is some softclipping for local alignment included by default. Supposedly this can be deactivated by using the parameters

-o FullNW

I have been trying to run novoalign with the following command line, in order to deactivate the softclipping:

novoalign -o SAM -o FullNW -d ref.ndx -f fastq1 fastq2 > file.sam

The above command runs fine and returns absolutely no errors. BUT, I feel like it is extremely suspicious that the run time is EQUAL regardless of -o FullNW for the same fastq files.

If you are turning off the local alignment step, shouldn't the mapping take much less time?

I am still new to NGS, and it probably shows

You're right that it doesn't make a noticeable difference. The alignment process is virtually the same in that the alignment location and score are determined by Needleman-Wunsch algorithm. Most of the alignment time is taken finding the best alignment location. We may seed to 10,000's of locations to find one good alignment. Having found the best alignment it is trimmed back to best local alignment but this only happens at the alignment location being reported so it becomes a very small % of cpu time, 1 :: 10,000 of total time.

Colin