Clarify terminology with respect to unpaired/SE reads

[bede]

References to unpaired reads in the CLI help and README are potentially ambiguous, possibly interpreted as reads lacking a mate for QC reasons or otherwise. It is intended to refer to single end (SE) short reads, for instance Illumina reads that have been merged. This should be reviewed and clarified. Highlighted by @jfy133 (#46).

[bede]

In 9634e7a I've replaced references to "unpaired" reads with "single/unpaired". I've also clarified the behaviour of the default --aligner auto in the CLI help.

[jfy133]

I think that would help future me yes, thank you @bede !