Skip to main content

Table 2 Summary of pangene analyses based on minimap2 whole genome alignments (WGA). N50 values, that describe the length of aligned genomic fragments, are shown as ranges of observed [min, max] values. The percentage of genes in blocks of 3 + contiguous genes is also shown as a range. Note that barley and wheat datasets require optional argument -H, which masks geneless regions longer than 1Mbp, where repeated sequences accumulate. Maximum RAM use was measured for pairwise WGA batch jobs

From: GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

 

Max RAM (GB)

WGA N50 (Kbp)

% Genes blocks3 + 

Total clusters

(Soft) core clusters

% BUSCO complete

ACK2

4.5

6.1

34.0

38,785

20,647

94.1

rice3

1.4

[27.4, 29]

[75.1, 77.8]

61,913

19,170

85.2

chr1wheat10 (-H)

64.5

[80.8, 142.4]

[38.8, 53.8]

25,280

9937

 

barley20 (-H)

46.3

[43.6, 75.7]

[25.4, 35.3]

165,544

23,811 (29, 226)

86.6 (95.3)