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Table 8 Comparison of sequencing platform, assembler, and assembly statistics for the reptiles for which a genome sequence is available

From: High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps

 

Bearded dragon

Burmese python

King cobra

Saltwater crocodile

Chicken

Green anole

American alligator

Gharial

Chinese softshell turtle

Green sea turtle

Western painted turtle

Pogona vitticeps

Python bivittatus

Ophiophagus hannah

Crocodylus porosus

Gallus gallus

Anolis carolinensis

Alligator mississippiensis

Gavialis gangeticus

Pelodiscus sinensis

Chelonia mydas

Chrysemys picta

Assembler

SOAP deNovo

SOAP deNovo

CLC NGS Cell (version 2011)

AllPaths (version R41313)

Celera Assembler (version 5.4)

Arachne (version 3.0.0)

Allpaths (version R41313)a

SOAP deNovo

SOAP deNovo

SOAP deNovo

Newbler

Sequence method

Illumina HiSeq 2000

Illumina GAIIx & HiSeq 2000, Roche 454

Illumina HiSeq

Illumina GAII & HiSeq 2000

Sanger, Roche 454

Sanger

Illumina GAII & HiSeq 2000

Illumina GAII

Illumina HiSeq 2000

Illumina HiSeq 2000

Roche 454, Illumina, Sanger

Average read depth

85.5X

20X

28X

74X

12X

7.1X

68X

109X

105.6X

110X

15X

Genome size (Gbp)

1.77

1.44

1.36–1.59

2.12

1.20

 

2.17

2.88

2.21

2.24

2.6

Total bases in contigs (excluding unknown bases, Ns)

1,747,541,145

1,384,532,810

1,380,486,984

2,088,185,434

1,032,841,023

1,701,336,547

2,129,643,287

2,198,585,703

2,106,622,020

2,110,365,500

2,173,204,098

Total bases in scaffolds

1,816,115,349

1,435,035,089

1.66 Gbp

2,120,573,303

1,046,932,099

1,799,143,587

2,174,259,888

2,270,567,745

2,202,483,752

2,208,410,377

2,365,766,571

No. of scaffolds (>100 bp)

543,500

39,113

-

23,365

16,847

6,645

14,645

9,317

19,904

140,023

78,631

N50 scaffold (kbp)

2,291

214

226

204

12,877

4,033

509

2,188

3,351

3,864

6,606

No. of contigs (>100 bp)

636,524

274,244

816,633

112,407

27,041

41,986

114,159

177,282

205,380

274,367

262,326

N50 contig (kbp)

31.2

10.7

5.2

32.7

279

79.9

36

23.4

22.0

29.2

21.3

Repeat content

39.5

31.8

35.2

37.5

9.4

34.4

37.7

37.6

42.47

37.35

9.82

No. protein-coding genes

19,406

17262

-

13,321

15,508

17,472

23,323

14,043

19,327

19,633

--

  1. Information is taken from the NCBI database (http://www.ncbi.nlm.nih.gov/assembly), with additional data from the primary papers in which the findings were originally published. aManual scaffolding
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