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NovoSort

Custom designed multi-threaded sort/merge tools for BAM files.

 

Packed with features:

  1. Reduced run times from multi-threading and by combining sort & merge 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. Optionally create 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

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