Packed with features:

1. Reduced run times from multi-threading and by combining sort,merge & index creation in one step.
2. Mark duplicates while you sort.
3. Option to included strand as part of the sort key.
4. Picard like handling of @PG and @RG identifiers
5. Uses a stable sort/merge algorithm that will not change the order of alignments with the same sort key.
6. Option to add or replace @RG record
7. Smart handling of @SQ records means order does not have to be the same in files being merged.
8. Creates BAM index file.

“Re-sorting aligned files by read position … is a common task. The fastest algorithm to our knowledge is Novosort … This algorithm is so efficient that it saturated the peak node injection bandwidth on Blue Waters (9.6GB/s)”

Mainzer et al, Instrumenting Human Variant Calling Workflow, Blue Waters 2015 Annual Report