Evaluate the Performance of sequence-to-graph mapping in GraphAligner.

[gsc74]

I want to evaluate the Performance of sequence-to-graph mapping as shown in Table 2 in minigraph, for both minigraph and GraphAligner, I'm able to get numbers for minigraph with using paftools.js mapeval minigraph_output.gaf. [paftools.js] Output: Q 60 2778043 13768 0.004956007 2778043 Q 59 828 7 0.004957049 2778871 Q 58 794 6 0.004957792 2779665 Q 57 754 6 0.004958605 2780419 Q 56 838 5 0.004958909 2781257 Q 55 756 4 0.004958999 2782013 ........ ........ While using same command paftools.js mapeval GraphAligner_output.gaf Output : Q 60 2907330 2907330 1.000000000 2907330 Q 58 1 1 1.000000000 2907331 Q 56 18 18 1.000000000 2907349 ............ ............. @maickrau , I want to know what is the difference between gaf output of minigraph and GraphAligner, and why paftools.js is giving right numbers for minigraph while wrong numbers for GraphAligner. How do i evaluate number of unmapped reads and wrong mappings in GraphAligner.

[ekg]

This might be a question to ask the paftools author, who made the table in question.