Relative orientation of the reads

For all codes, it is possible to assemble the pair to any of the two reference sequence strands, so `ff' may mean that both reads are placed in the forward direction or that both reads are placed in the reverse direction. There is still a difference between `ff' and `bb', though. For `bb', the second read is effectively placed before the first read. The 'bb' option is not widely used and is included for the sake of completeness.

The allowed values for the directions and their meanings are summarized in the table below.

Code First Second Description
ff $ \rightarrow$ $ \rightarrow$ Both reads are forward.
fb $ \rightarrow$ $ \leftarrow$ Reads point toward each other.
bf $ \leftarrow$ $ \rightarrow$ Reads point away from each other.
bb $ \leftarrow$ $ \leftarrow$ Both reads are backward.