I've added a rough implementation of BBMap for the mapping step in consensus generation. The default is still to use BWA as before, but for those who want to control the stringency of mapping, BBMap allows a minid parameter that is default 0.95 in my implementation (but can be changed by passing a -m option).
I've also cleaned up the formatting and a few minor typos.
I've added a rough implementation of BBMap for the mapping step in consensus generation. The default is still to use BWA as before, but for those who want to control the stringency of mapping, BBMap allows a
minidparameter that is default 0.95 in my implementation (but can be changed by passing a-moption). I've also cleaned up the formatting and a few minor typos.