how to interpret yak inspect to evaluate the completeness of an assembly

[Ashleyfarlow]

Thank you for this tool. After running:

yak count -b37 -t4 -o sr.yak myreads.fq.gz
yak count -b37 -t4 -o scaffold.yak scaffold.fa
yak inspect sr.yak scaffold.yak > sr-scaffold.kqv.txt

I obtain these results in sr-scaffold.kqv.txt:

...
SN      5       29997294        2943642 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  0.0000
SN      4       54814313        5427049 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  0.0000
SN      3       119820206       12359127        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  0.0000
SN      2       577560021       57889442        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  0.0000
QV      20      1686753367      1686676513      4.915   -1.000
QV      19      1806056255      1805978021      4.893   -1.000
QV      18      1918241646      1918162190      4.874   -1.000
QV      17      2021819785      2021739232      4.857   -1.000
QV      16      2115831944      2115750327      4.843   -1.000
QV      15      2199727376      2199644874      4.831   -1.000
QV      14      2273569360      2273486096      4.821   -1.000
QV      13      2337885508      2337801575      4.813   -1.000
QV      12      2393381989      2393297514      4.806   -1.000
QV      11      2441048817      2440963948      4.799   -1.000
QV      10      2481791146      2481705971      4.794   -1.000
QV      9       2516588006      2516502574      4.789   -1.000
QV      8       2546760834      2546675206      4.785   -1.000
QV      7       2573349003      2573263248      4.781   -1.000
QV      6       2600045275      2599959418      4.778   -1.000
QV      5       2630042569      2629956665      4.773   -1.000
QV      4       2684856882      2684770932      4.764   -1.000

How should I interpret these results (this is a human assembly from pacbio, and the short reads are 80x illumina).

[ASLeonard]

I am also wondering how to interpret these results, as mine are similar. From the inspect.c code, it appears the QV lines are written by printf("QV\t%d\t%ld\t%ld\t%.3f\t%.3f\n", i, (long)qs.tot, (long)acc[i * YAK_N_COUNTS], qs.qv_raw, qs.qv);

It may be a different meaning, but otherwise there must be some issue giving a negative QV. Also I'm not sure how to determine the assembly completeness from these values.