prophyle/prophex

Masking repeated k-mers

Opened this issue · 0 comments

karel-brinda commented

Description

It would be nice to have an option for masking those k-mers that are repeated in the read (only the first occurrence of the k-mer would be reported).

Example:

  • ref: 
    >node
AAA
  • read AAAAAAAAAAAAAAAAAAAA, k=3, output: node:1 M:16 instead of node:17