lh3 / yak

Yet another k-mer analyzer
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Understanding output of yak inspect for completeness #20

Open nirvana693 opened 1 year ago

nirvana693 commented 1 year ago

As mentioned in the manual, I have checked the read k-mer profile vs assembly k-mer profile using yak inspect. The output file contains lines starting with SNand QV.

SN      2       588933275       66784153        0.0007  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000 0.0000   0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
QV      20      2507879712      2505578138      6.467   -1.000
QV      19      2526259992      2523952802      6.464   -1.000
QV      18      2542258425      2539946329      6.461   -1.000
QV      17      2555656121      2553339972      6.459   -1.000
QV      16      2566448967      2564129690      6.457   -1.000
QV      15      2574901954      2572580226      6.456   -1.000
QV      14      2581364686      2579041194      6.455   -1.000
QV      13      2586262378      2583937639      6.454   -1.000
QV      12      2590120298      2587794660      6.453   -1.000
QV      11      2593472460      2591146198      6.452   -1.000
QV      10      2596865531      2594538820      6.452   -1.000
QV      9       2600840467      2598513407      6.451   -1.000
QV      8       2606142321      2603814977      6.450   -1.000
QV      7       2614002259      2611674634      6.448   -1.000
QV      6       2626876357      2624548450      6.445   -1.000
QV      5       2650645186      2648316963      6.439   -1.000
QV      4       2702958740      2700630199      6.428   -1.000
QV      3       2849803532      2847474729      6.395   -1.000
QV      2       3438736807      3436407745      6.282   -1.000

Could you please help understand the output fields and how to calculate the completeness? Other outputs (qv, trioeval) from yak have header describing these fields.

Thank you