SAM/BAM format v1.5 extensions for de novo assemblies.The current version is a terse three pages (trying to meet an "application note" page limit), but nevertheless should clarify the intended usage of these parts of the SAM/BAM specification.
Peter J. A. Cock, James K. Bonfield, Bastien Chevreux, Heng Li.
bioRxiv DOI: 10.1101/020024
Here's a little back-story on my latest preprint (based on my email to samtools-devel), which went live on the biology preprint server bioRvix at the end of last week: