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ratschlab / metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
http://metagraph.ethz.ch
GNU General Public License v3.0
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Alignment output #460

Closed Glfrey closed 1 year ago

Glfrey commented 1 year ago

Hello again, long time no posting!

I'm revisiting some of my older work and I just wanted to clarify the output of metagraph align. What are the different column headers? I've put the ones I can figure out below

  1. Query name
  2. Query sequence
  3. Strand
  4. Reference sequence
  5. ?
  6. ?
  7. CIGAR string-like alignment summary
  8. ?
  9. Ref name matches

Could you help me fill in the bits I'm missing?

Thank you as always!

hmusta commented 1 year ago

@Glfrey The ones you've guessed so far are right, here's the whole list:

  1. Query name
  2. Query sequence
  3. Strand
  4. Reference sequence
  5. Alignment score
  6. Number of exact matches
  7. CIGAR string-like alignment summary
  8. Number of nucleotides trimmed from the prefix of the reference sequence
  9. Ref name matches

Column 8 only really applies if you have a short alignment that's less than the graph k, where you can have an alignment where only the suffix of a node's spelling is matched.