I originally asked: Are sequencing methods consistent in how their report which is the "forward" strand and which is the "reverse" strand or this in an arbitrary choice?
It has been pointed out that this question is unclear, since it could mean both: (i) NGS sequencing and the strand from which a given read might come from or (ii) the designation of one strand as 'forward' and one strand as 'reverse' in the description of a double-stranded DNA. I meant to ask for (ii) and although, in retrospective, I can see that (i) is likely interpretation given how I phrased the question.
Now I actually found two other biostar questions which are similar to this: 1) http://www.biostars.org/post/show/3423/forward-and-reverse-strand-conventions/ and 2) http://www.biostars.org/post/show/3908/conventions-for-designating-forward-and-reverse-strands/
I am still a little confused nevertheless. An highly up-voted answer to 1) says "The designation is arbitrary" while 2) seems to indicate that there is indeed a convention for human chromosomes. I am still wondering, though, what then about the circular bacterial chromosome. Is the designation arbitrary in that case?
I don't believe that bacterial chromosomes have any biologically significant "polarizing" features that would give any kind of inherent directionality to the origin of replication. As far as I'm aware, replication begins at the origin of replication symmetrically and proceeds in both directions along the chromosome. So any kind of strand designation would necessarily be arbitrary, because there is not inherent strandedness to a circular chromosome. For linear chromosomes, the choice also seems to be arbitrary. In theory things could be chosen so that the plus strand always starts closest to the centromere, and this is the case in all the human chromosomes, but as you have noticed, it is not the case for other organisms.
There is no contradiction between saying that there is a convention and that the conventional designation is arbitrary.