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Table 8 Time and memory usage for overlap extension and assembly on viral metagenomic data from human plasam

From: TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

  

Time (m: minutes, h: hours)

Memory (GB)

Mismatch rate

5%

10%

15%

20%

5%

10%

15%

20%

Overlap extension

Building index

127m

127m

127m

127m

2.4

2.4

2.4

2.4

 

Recruitment

8m

14m

20m

23m

3.5

3.5

3.5

3.5

De novo Assembly

TAR-VIR

5m

7m

18m

20m

2

2.8

3.5

4

 

SGA

2m

2m

3m

5m

0.9

0.9

0.9

0.9

 

SPAdes

5m

5m

6m

8m

1

1

1

1

 

SAVAGE

2h

8h

14h

18h

31

45

51

59

Reference-based assembly

HaploClique

  

33h

   

5

 
 

Viquas

  

72h

   

4

 
 

drVM

  

23m

   

1

 

Extension-based assembly

PRICE

  

1h46m

   

5

 
  1. The de novo assembly time and memory usage were evaluated on recruited reads based on mismatch rate from 5% to 20%. HaploClique, Viquas, drVM and PRICE were applied only on recruited reads based on mismatch rate of 15%
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BMC Bioinformatics

ISSN: 1471-2105

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