While running abyss-pe, I would often get this message printed to stdout.
Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 9840128 12.3% Singleton 20579451 25.7% FR 28709736 35.9% RF 20287 0.0253% FF 130290 0.163% Different 20752726 25.9% Total 80032618 Ambiguous paths: 86 Merged: 48 No paths: 0 Too many paths: 4 Too complex: 1 Dissimilar: 33
I thought that these represented the percentage of original reads mapped to the scaffold produced by abyss, but the total is greater than the number of original reads. Also, I would appreciate any information or literature regarding the meaning of FR, RF, FF and Singleton.
Thanks a lot!