R. sphaeroides

Revision as of 01 August 2013 02:32 by admin (Comments | Contribs)

Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of a circular chromosome of 3,188,609 bp and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively.


Read source

The paired-end illuminia read data of R. sphaeroides were downloaded from Gage-B

Sequence assembly

There are eight assemblers, ABySS, CABOG, MaSuRCA, MIRA, SGA, SOAPdenovo, SPAdes 2.5 and Velvet, used in the data, and the scaffolding results were downloaded from SPAdes website

Contig integrator

Contigs

Evaluation

  • Benchmark genome
R. sphaeroides 2.4.1
  • Evaluated by QUAST
QUAST (QUAST v2.1)
Running QUAST needs gene and sequence information.
Basic statisitcs ABySS CABOD MaSuRCA SGA SOAPdenovo SPAdes 2.5 Velvet CISA
# contigs 382 131 52 733 185 40 143 35
Largest contig 71578 177098 241348 44874 204500 739647 236829 740054
Total length 4503182 3953489 4247061 4091078 4549335 4781613 4526809 4950301
NG50 21441 40287 144812 7971 45133 518052 85272 523557
Misassemblies
# misassemblies 4 15 15 3 1 3 9 11
Misassembled contigs length  155883 1987058 765654 24763 90965 94799 723259 2399227
Genome statistics
Genome fraction (%) 98.444 99.334 99.009 97.438 98.099 98.554 97523 99.38
# genes 5819 + 64 part  5965 + 34 part  5964 + 34 part  5635 + 231 part  5839 + 44 part  5950 + 27 part  5604 + 275 part  5980 + 28 part 
# mismatches per 100 kbp 6.62 4.43 8.96 0.7 8.16 2.07 5.93 6.08'
# indels per 100 kbp 7.57 5.86 5.95 2 5.69 2.39 30.28 2.78
# N's per 100kbp 116.43 17.43 7.49 0 8.51 15.24 783.91 0.04