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Table 1 Output parameters of de novo assembly and mapping.

From: NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective

  

Mapping

De novo assembling

  

BTL

BBM

High sensitivity

Low sensitivity

C. albicans CMC 1853 23,810 reads

n° reads assembled

23,389

22,755

23,721

23,674

 

n° reads not assembled

421

1,055

89

136

 

Assembly duration

7.19 seconds

21.58 seconds

38 minutes-10 seconds

12 minutes-29 seconds

 

CPU time

8.54 seconds

12.49 seconds

2h-11 minutes

41 minutes-15 seconds

 

Contigs

1

1

119

219

C. albicans CMC 1856 53,497 reads

n° reads assembled

52,270

51,599

52,187

53,022

 

n° reads not assembled

1,227

1,898

1,310

475

 

Assembly duration

11.47 seconds

33.06 seconds

47 minutes+34 seconds

10 minutes-46 seconds

 

CPU time

13.37 seconds

17.31 seconds

2h-49 minutes

34 minutes-1 second

 

Contigs

1

1

242

357

C. glabrata CMC 1837 19,762 reads

n° reads assembled

18,883

18,257

19,454

19,334

 

n° reads not assembled

879

1,505

308

428

 

Assembly duration

5.10 seconds

21.01 seconds

26 minutes-10 seconds

10 minutes-8 seconds

 

CPU time

6.68 seconds

10.52 seconds

1h-33 minutes

34 minutes-2 seconds

 

Contigs

1

1

121

209

C. glabrata CMC 1934 49,337 reads

n° reads assembled

47,611

46,352

48,897

48,479

 

n° reads not assembled

1,726

2,985

440

858

 

Assembly duration

10.48 seconds

34.93 seconds

1h-40 minutes

21 minutes-11 seconds

 

CPU time

11.48 seconds

21.11 seconds

5h-20 minutes

1h-11 minutes

 

Contigs

1

1

243

470

C. orthopsilosis CMC 1880 20,089 reads

n° reads assembled

19,533

19,472

19,960

19,923

 

n° reads not assembled

556

617

129

166

 

Assembly duration

7.69 seconds

27.36 seconds

34 minutes-27 seconds

11 minutes-5 seconds

 

CPU time

10.98 seconds

22.71 seconds

1h-58 minutes

37 minutes-37 seconds

 

Contigs

1

1

119

236

C. orthopsilosis CMC 2011 36,955 reads

n° reads assembled

36,136

36,019

36,720

36,591

 

n° reads not assembled

819

936

235

364

 

Assembly duration

11.45 seconds

38.25 seconds

59 minutes-5 seconds

15 minutes-47 seconds

 

CPU time

7.91 seconds

14.50 seconds

3h-20 minutes

51 minutes-58 seconds

 

Contigs

1

1

219

477

C. parapsilosis CMC 1838 37,683 reads

n° reads assembled

36,717

36,584

37,683

37,432

 

n° reads not assembled

966

1,099

1,264

251

 

Assembly duration

12.19 seconds

27.66 seconds

44 minutes-3 seconds

15 minutes-11 seconds

 

CPU time

17.55 seconds

29.27 seconds

2h-33 minutes

51 minutes-48 seconds

 

Contigs

1

1

190

335

C. parapsilosis CMC 2039 23,817 reads

n° reads assembled

21,549

21,502

22,569

22,336

 

n° reads not assembled

2,268

2,315

1,248

1,481

 

Assembly duration

7.24 seconds

19.88 seconds

41 minutes-34 seconds

32 minutes-57 seconds

 

CPU time

5.73 seconds

11.48 seconds

2h-24 minutes

1h-1 minute

 

Contigs

1

1

281

632

C. tropicalis CMC 2003 44,744 reads

n° reads assembled

41,841

41,361

43,253

44,140

 

n° reads not assembled

2,903

3,383

1,491

604

 

Assembly duration

12.23 seconds

31.09 seconds

43 minutes-4 seconds

15 minutes-9 seconds

 

CPU time

9.70 seconds

14.13 seconds

2h-28 minutes

45 minutes-59 seconds

C. tropicalis CMC 2017 20,125 reads

n° reads assembled

18,007

17,593

19,671

19,550

 

n° reads not assembled

2,118

2,532

454

575

 

Assembly duration

6.07 seconds

22.98 seconds

33 minutes-32 seconds

11 minutes-47 seconds

 

CPU time

5.45 seconds

8.12 seconds

1h-56 minutes

39 minutes-35 seconds

 

Contigs

1

1

369

527

M. guilliermondii CMC 1825 40,659 reads

n° reads assembled

36,085

35,598

40,094

39,914

 

n° reads not assembled

4,574

5,061

565

745

 

Assembly duration

12.25 seconds

27.05 seconds

51 minutes-46 seconds

19 minutes-55 seconds

 

CPU time

15.88 seconds

15.43 seconds

2h-58 minutes

1h-5 minutes

 

Contigs

1

1

507

711

M. guilliermondii CMC 1924 19,388 reads

n° reads assembled

17,593

17,335

19,195

19,152

 

n° reads not assembled

1,795

2,053

193

236

 

Assembly duration

6.33 seconds

19.18 seconds

22 minutes-39 seconds

9 minutes-18 seconds

 

CPU time

7.02 seconds

9.02 seconds

1h-20 minutes

31 minutes-10 seconds

 

Contigs

1

1

129

248