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Table 3 Comparison of Readjoiner and LEAP

From: Readjoiner: a fast and memory efficient string graph-based sequence assembler

 

RJ

LEAP

LEAP RJ

RJ

LEAP

LEAP RJ

RJ

LEAP

LEAP RJ

RJ

RJ

Read set

c22

c22

-

c2

c2

-

hg20×

hg20×

-

hg30×

hg40×

Genome size (Mbp)

34.9

34.9

-

238.2

238.2

-

2861.3

2861.3

-

2861.3

2861.3

Number of reads (M)

7.0

7.0

-

47.6

47.6

-

579.5

579.5

-

869.2

1155.3

Overall time

6 min

9 min

1.60×

53 min

1 h 36 min

1.81×

20 h 4 min

35 h 56 min

1.79×

34 h 9 min

51 h 16 min

Overall space (GB)

0.3

0.9

2.99×

2.0

4.0

1.98×

27.9

45.6

1.63×

39.8

52.0

Contigs

120712

113428

-

634403

630408

-

3239309

11662607

-

13497497

16253905

Total contigs length (Mbp)

45.7

43.1

-

292.2

280.6

-

2833.1

3642.7

-

4003.9

4281.1

Assembly N50 (Kbp)

1.6

1.6

-

3.2

3.0

-

3.0

1.4

-

1.2

0.9

Assembly NG50 (Kbp)

2.7

2.4

-

4.5

3.9

-

3.0

2.5

-

2.9

2.8

Longest contig (Kbp)

41.4

39.4

-

52.9

48.9

-

63.4

58.6

-

63.4

63.4

  1. Results of applying Readjoiner (RJ) and LEAP to the datasets c22, c2, hg20× , hg30× , hg40× (ℓ min  = 45). LEAP was not able to process hg30× and hg40× on the test machine with 64 GB RAM.