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Table 2 Simulation of AFLAP testing different genome and sequencing coverage variations. Maps aligned to assemblies in Additional file 1

From: AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Assembly size

Chromosomes

Cross structure

Simulated progeny sequencing depth

Simulated parental sequencing depth

Simulated heterozygosity

Segregating markers detected by AFLAP

Markers used in linkage analysis

Minimum LOD score

Linkage groups calculated

Percent of markers placed in linkage groups

Collinearity of genetic map with genome assembly (average Kendall rank coefficient; τ)

Run time (wall clock)

i) Altering progeny sequencing depth.

 119 Mb

5

F1 (ABxCC)

20

50

0.2%

186,522

10,000

7

5

100%

0.993

8 h 44 min

 119 Mb

5

F1 (ABxCC)

10

50

0.2%

186,523

10,000

7

5

99.8%

0.986

6 h 13 min

 119 Mb

5

F1 (ABxCC)

7

50

0.2%

186,523

10,000

7

5

> 99.9%

0.988

5 h 18 min

 119 Mb

5

F1 (ABxCC)

5

50

0.2%

186,525

10,000

7

5

98%

0.983

4 h 22 min

 119 Mb

5

F1 (ABxCC)

3

50

0.2%

186,525

10,000

3

6

86.7%

0.826

4 h 17 min

ii) Altering parental sequencing depth.

 119 Mb

5

F1 (ABxCC)

10

50

0.2%

186,523

10,000

7

5

99.8%

0.986

6 h 13 min

 119 Mb

5

F1 (ABxCC)

10

40

0.2%

189,329

10,000

7

5

99.8%

0.985

6 h 5 min

 119 Mb

5

F1 (ABxCC)

10

30

0.2%

179,218

10,000

7

5

99.8%

0.985

6 h 20 min

 119 Mb

5

F1 (ABxCC)

10

20

0.2%

127,628

10,000

7

5

99.8%

0.985

6 h 0 min

 119 Mb

5

F1 (ABxCC)

10

10

0.2%

112,655

10,000

7

5

99.8%

0.986

5 h 40 min

iii) Altering parental heterozygosity.

 119 Mb

5

F1 (ABxCC)

10

50

0.01%

9996

9996

7

5

99.8%

0.985

6 h 49 min

 119 Mb

5

F1 (ABxCC)

10

50

0.1%

97,446

10,000

7

5

99.8%

0.984

7 h 3 min

 119 Mb

5

F1 (ABxCC)

10

50

0.2%

186,523

10,000

7

5

99.8%

0.986

6 h 13 min

 119 Mb

5

F1 (ABxCC)

10

50

0.5%

401,020

10,000

7

5

99.8%

0.983

7 h 6 min

 119 Mb

5

F1 (ABxCC)

10

50

1%

736,293

10,000

7

5

99.6%

0.984

6 h 40 min

 119 Mb

5

F1 (ABxCC)

10

50

2%

1,148,814

10,000

7

5

99.2%

0.984

7 h 12 min

iv) Altering genome size and chromosome number.

119 Mb

5

F1 (ABxCC)

10

50

0.2%

186,523

10,000

7

5

99.8%

0.986

6 h 13 min

500 Mb

19

F1 (ABxCC)

10

50

0.2%

490,397

50,000

7

19

99.2%

0.984

12 h 23 min

900 Mb

9

F1 (ABxCC)

10

50

0.2%

801,712

25,000

7

9

99.3%

0.982

22 h 0 min

v) Altering cross type

 119 Mb

5

F1 (ABxCC)

10

50

0.2%

186,523

10,000

7

5

99.8%

0.986

6 h 13 min

 119 Mb

5

F2 (AAxCC)

10

50

0%

94,428

104,106

10,000

10,000

7

7

5

5

100%

> 99.9%

0.978

0.977

7 h 49 min