Optimize indel-heavy consensus assembly

Question

Optimize indel-heavy consensus assembly

mikessh opened this issue 9 years ago · 2 comments

Answer 1 · 2015-08-25T14:57:02.000Z

Connected to https://github.com/milaboratory/milib/issues/18 or not?

Answer 2 · 2015-08-25T15:08:12.000Z

@dbolotin nope :( Need to add specific handling for non-matching (x+ consequent mismatches) reads in seed-based multiple alignment algorithm used for MIGs. The original algorithm will not tolerate indels (even 1bp) and drop such reads. In case of indel-heavy (by # indels/read, not their length, etc) data (454/torrent) this will cause lots of information to be lost.