TODO: Run -nodovetail run and compare results: How often does dovetailing happen?
no-mixed: By default, when bowtie2 cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior.
--no-discordant: By default, bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior.
Allow one mate alignment to contain another: False
Allow mate alignments to overlap: False
Overlapping and containing ok for an alignment to be concordant, dovetailing not ok
See http://www.cureffi.org/2012/12/19/forward-and-reverse-reads-in-paired-end-sequencing/ for a nice discussion
