You can specify that a read file came from a paired sequencing experiment using the `-p' option. This option is described in detail here, as well as within the read mapping and de novo assembly sections of the manual.
A typical set of information one would provide after the -p flag would look like this
-p fb ss 100 200. The meaning of this would be:
- fb Specifies the relative orientation of the reads. Here, the first read of the pair is in the forward direction, the second read is in the backward, or reverse, orientation. The allowed values for this are provided below.
- ss Specifies the way the distances between the pair members should be measured. Here, the distances are given from the start (5 prime end) of the first read to the start (5 prime end) of the second read. Here, since the relative orientation is set to fb, the second read is reversed, so indicating ss means that the distance specified will include both the read lengths as well as the length of the sequence between the reads.
- 100 200 The range of distances expected between the specified start positions. Here this is between 100 and 200 bases.