smarco/WFA-paper

Prefer match over long gap at the front or end of alignment

slw287r opened this issue · 2 comments

slw287r commented

I've long paired-end data which has a great portion of overlaps. I tried your wonderful aligner it returned some of results out of my expectation. I'm still in vain after tuning up the penalties for gap open and extension. Is it possible for me to get the preferred alignment?

  • WFA alignment
  SCORE COMPUTED -28      PRETTY.ALIGNMENT
      PATTERN    CTGT----GCGTTGGATTCCTTACTGTGAAATGGAGATAACAAATAAACCCACCTCCTGGTGTTGCTTTGATGATTAAATGAGCTGAGTGTAACAAGCTCAACTAATGTTAGTTAGTCATAATGATCCAGAATGCAGTTACTC
                 ||||    |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
      TEXT       CTGTCTGTGCGTTGGATTCCTTACTGTGAAATGGAGATAACAAATAAACCCACCTCCTGGTGTTGCTTTGATGATTAAATGAGCTGAGTGTAACAAGCTCAACTAATGTTAGTTAGTCATAATGATCCAGAATGCAGTT----
  SCORE COMPUTED -248      PRETTY.ALIGNMENT
      PATTERN    TACTCTGACTCCAGAGTTTGTGCTGTTAAATACGTTGCTATCGTTCTACAGTTTGATTTTAAATTGCTATTTTTACTCATACTGTGGACTGCTCATCCTTTGCTCTTTTTTTCTTTAACAAAGAATTTTCTCAGTATTCTAATCTTGTACTTAAGGTAATTGTTTATATTATGTAAGTTATTTCTATTATTAAG-----------------------------------------------------------
                 ||                                                           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                                           
      TEXT       TA-----------------------------------------------------------AATTGCTATTTTTACTCATACTGTGGACTGCTCATCCTTTGCTCTTTTTTTCTTTAACAAAGAATTTTCTCAGTATTCTAATCTTGTACTTAAGGTAATTGTTTATATTATGTAAGTTATTTCTATTATTAAGTAAAATAATCTGTGTGCTATAGAAAACACCAAGATTCAGGTTGAATTTCCATCCAAGGG
  • My personally favored alignment
      PATTERN    ----CTGTGCGTTGGATTCCTTACTGTGAAATGGAGATAACAAATAAACCCACCTCCTGGTGTTGCTTTGATGATTAAATGAGCTGAGTGTAACAAGCTCAACTAATGTTAGTTAGTCATAATGATCCAGAATGCAGTTACTC
                     |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
      TEXT       CTGTCTGTGCGTTGGATTCCTTACTGTGAAATGGAGATAACAAATAAACCCACCTCCTGGTGTTGCTTTGATGATTAAATGAGCTGAGTGTAACAAGCTCAACTAATGTTAGTTAGTCATAATGATCCAGAATGCAGTT----
  SCORE COMPUTED -248      PRETTY.ALIGNMENT
      PATTERN    TACTCTGACTCCAGAGTTTGTGCTGTTAAATACGTTGCTATCGTTCTACAGTTTGATTTTAAATTGCTATTTTTACTCATACTGTGGACTGCTCATCCTTTGCTCTTTTTTTCTTTAACAAAGAATTTTCTCAGTATTCTAATCTTGTACTTAAGGTAATTGTTTATATTATGTAAGTTATTTCTATTATTAAG-----------------------------------------------------------
                                                                            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                                           
      TEXT       -----------------------------------------------------------TAAATTGCTATTTTTACTCATACTGTGGACTGCTCATCCTTTGCTCTTTTTTTCTTTAACAAAGAATTTTCTCAGTATTCTAATCTTGTACTTAAGGTAATTGTTTATATTATGTAAGTTATTTCTATTATTAAGTAAAATAATCTGTGTGCTATAGAAAACACCAAGATTCAGGTTGAATTTCCATCCAAGGG

Thanks,
Richard

smarco commented

Hi, Richard.

I see that what you want here is "ends-free" alignment. The current version of WFA (in accordance with the description on the Bioinformatics paper) implements "global-alignment". Nonetheless, extension of the WFA to "ends-free", "semi-global" or similar is quite straightforward. I am marking this as a "feature request" and I will make sure it is added on the next version.

I hope this helps.

  • 👍2
slw287r commented

This helps a lot!
Thank you.