Table 1 Comparison of AFLAP with a conventional linkage analysis pipeline. Maps aligned to assemblies in Additional file 1
From: AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
Method | Assembly size | Chromosomes | Segregating markers detected. | Markers used in linkage analysis. | Minimum LOD score | Linkage groups calculated | Map length estimated | Percent of markers placed in linkage groups (%) | Collinearity of genetic map with genome assembly (average Kendall rank coefficient; Ï„) | Run time (wall clock) |
|---|---|---|---|---|---|---|---|---|---|---|
AFLAP | 119 Mb | 5 | 186,523 | 186,523 | 7 | 5 | 699 cM | 99.8 | 0.986 | 59 h 32 min |
AFLAP | 119 Mb | 5 | 186,523 | 10,000 | 7 | 5 | 696 cM | 99.8 | 0.986 | 6 h 13 min |
Conventional | 119 Mb | 5 | 225,797 | 225,797 | 20 | 5 | 701 cM | 99.6 | 0.992 | 173  34 min |
Conventional | 119 Mb | 5 | 226,087 | 10,000 | 7 | 5 | 698 cM | 99.8 | 0.992 | 107 h 5 min |