Advanced options: to produce alignments in favor of substitutions instead of short indels. - pb-cdunn/blasr GitHub Wiki

In order to produce alignments which in favor of substitutions instead of short indels (insertions/deletions), you may want to increase indel penalties by specifying '-insertion' and '-deletion' options. The default insertion and deletion penalties are 4 and 5, respectively. Increasing the values leads to more indel penalties.

For example, the following commands produce slightly different alignments.

$ blasr reads.fa ref.fa -m 0

  0  GGGCGGCGACCTCGCGGGTTTGT-GCTATTTATGAAAATTTTCCGGTTTA
     ||||||||||||||||||||| | ||||||||||||||||||||||||||
  0  GGGCGGCGACCTCGCGGGTTT-TCGCTATTTATGAAAATTTTCCGGTTTA

 49  AGGCGTTTCCGTTCTGGTTCGTCATAACTTAATGGGTTTATTTAAAATAC
     |||||||||||||||**|||||||||||||||||**||||||||||||||
 49  AGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATAC

 99  CCTCTG-AAA-AAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTAGGCCT
     |||||| ||| |||||||||||||||||||||||||||||||||*|||||
 99  CCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCT

147  CTGTCGTTTCCTTTCTCTG--TTTGTCCGTGGAAT--ACAATGGAAGTCA
     |||||||||||||||||||  ||||||||||||||  |||||||||||||
149  CTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCA

193  ACAAAGAGCACG-TAGCCGGCATTTTCGGTGCGAGTATCCGTACCATTCA
     |||||*|||| | |*||*|*||||||||||||||||||||||||||||||
199  ACAAAAAGCA-GCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCA

242  GAACTGGCAGGAACAGTGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTA
     ||||||||||||||||*|||||||||||||||||||||||||||||||||
248  GAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTA

292  ATGA-G-GCTTTATGACTCTGCCGCCTTCATAAAATGGTATGCCGAAA-G
     |||| | |||||||||||||||||||*||||||||||||||||||||| |
298  ATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGG

339  G-TGCTGAAATT
     | ||||||||||
348  GATGCTGAAATT

$ blasr reads.fa ref.fasta -insertion 16 -deletion 20 -m 0

  0  GGGCGGCGACCTCGCGGGTTTGTGCTATTTATGAAAATTTTCCGGTTTAA
     |||||||||||||||||||||**|||||||||||||||||||||||||||
  0  GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAA

 50  GGCGTTTCCGTTCTGGTTCGTCATAACTTAATGGGTTTATTTAAAATACC
     ||||||||||||||**|||||||||||||||||**|||||||||||||||
 50  GGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACC

100  CTCTG-AAA-AAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTAGGCCTC
     ||||| ||| |||||||||||||||||||||||||||||||||*||||||
100  CTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTC

148  TGTCGTTTCCTTTCTCTG--TTTGTCCGTGGAAT--ACAATGGAAGTCAA
     ||||||||||||||||||  ||||||||||||||  ||||||||||||||
150  TGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAA

194  CAAAGAGCACGTAGCCGGCATTTTCGGTGCGAGTATCCGTACCATTCAGA
     ||||*||||**|*||*|*||||||||||||||||||||||||||||||||
200  CAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGA

244  ACTGGCAGGAACAGTGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAAT
     ||||||||||||||*|||||||||||||||||||||||||||||||||||
250  ACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAAT

294  GA-G-GCTTTATGACTCTGCCGCCTTCATAAAATGGTATGCCGAAA-GG-
     || | |||||||||||||||||||*||||||||||||||||||||| ||
300  GAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGA

340  TGCTGAAATT
     ||||||||||
350  TGCTGAAATT