Topic: how BowTie2 works

[crmackay]

people use this all the time, they generally use the defaults, or twiddle with the a few settings, but understanding how it actually aligns is important if you want to make informed conclusions from your data...

• a overview of how bowtie2 works
  • indexing ...maybe just indexing in general...the FM index and BWT could be another topic
  • mutliseed heuristics
  • extending seeds and backtracking
  • reporting the best alignment
  • default setting (seed length, seed spread, allows mismatched etc)
• potential problems
  • aligning to multiple genomes
  • seed sequences with gaps are not aligned
  • the best alignment is (semi)randomly chosen for multi-mappers