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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