Chop off sequences before aligment

Question

[Kitsune]

Hello!

I have a lot of sequences that have been obtained using different sets of primers. I want to align them, but first I have to remove that are not similar and won't align. Is there any way to do it automatically and not by hand? Thank you!!!

[GenoMax]

It is not clear what you want to do here.
As @b.nota says are you worried about parts of the reads that are not expected to align with the reference or are you referring to contaminants that may be full length reads?
In either case an aligner should be able to tackle those reads and handle them appropriately as long as you provide a correct reference.

Answer 1

[Benn]

To remove primer sequences, try cutadapt.

http://cutadapt.readthedocs.org/en/stable/guide.html