B. cereus

Revision as of 01 August 2013 20:29 by admin (Comments | Contribs) | (→Contig integrator)

Bacillus cereus strain ATCC_10987. The B. cereus ATCC_10987 consists of a circular chromosome of 5,224,283 bp and one plasmid of 208,369 bp in length, respectively.


Read source

The paired-end illumina read data of B. cereus were available at Gage-B.

Sequence assembly

We have downloaded the scaffolding assemblies of B. cereus from SPAdes website.

Contig integrator

We have used CISA to integrate the assemblies and generated CISA's contigs.

Evaluation

  • Benchmark genome
B. cereus ATCC_10987
  • Evaluated by QUAST
QUAST (QUAST v2.1)
Running QUAST needs gene and sequence information. There are 6014 genes in total.
Basic statisitcs ABySS CABOD MaSuRCA SGA SOAPdenovo SPAdes 2.5 Velvet CISA
# contigs 74 33 61 341 56 53 78 32
Largest contig 430487 1198056 1197734 106317 1194879 1202947 896381 1205706
Total length 5380708 5420940 5433046 5321914 5344353 5379795 5356258 5469099
NG50 135613 431479 337861 25512 456635 485493 247748 487570
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 97.523 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