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The SUGAR format

Sugar is Simple UnGapped Alignment Report, which displays ungapped alignments one-per-line. The sugar line starts with the string "sugar:" for easy extraction from the output, and is followed by the following 9 fields in the order below:

  1. query identifier
  2. query start position
  3. query stop position
  4. query strand
  5. target identifier
  6. target start position
  7. target stop position
  8. target strand
  9. score

Here an example of SUGAR format:

sugar: hs989235.cds 5 468 + hsnfg9.embl 25689 27450 + 1916

This format is used by Exonerate and seems to have been originaly developed for this tool. The format is related to the CIGAR format which add an extra (10th) field to describe Gaped alignment.