SPAdes - D1 and D5

Revision as of 14 August 2014 21:24 by admin (Comments | Contribs)

We used Dataset 1, E. coli K-12 MG1655 and single SMRT cell of Dataset 5


  • Evaluated by QUAST
QUAST (QUAST v2.3)
Running QUAST requires Ec_gene_list and NC_000913.fna. There are 4497 genes in total.
  • Score with QUAST: With PacBio Long Reads [ more detail]
Basic statistics Website data Raw Data Raw Data with D5 single SMRT cell
# contigs 1 14
Largest contig 4638970 4625005
Total length 4638970 4652215
N50 4638970 4625005
Misassemblies
# misassemblies 1 5
Misassembled contigs length 4638970 4625005
Mismatches
# mismatches per 100kbp 0.11 1.06
# indels per 100kbp 0.09 0.61
# N's per 100kbp 0 282.94
Genome statistics
Genome fraction (%) 99.983 99.418
Duplication ratio 1 1.013
# genes 4494 + 1 part 4471 + 2 part t
NGA50 4638970 2714032
Running Time 42m 2hr 35m

Misassemblies for Adobe reader.


  • Score with QUAST: Without PacBio Long Reads [ more detail]
Basic statistics Website data Raw Data
# contigs 2 1
Largest contig 4631220 4633080
Total length 4633146 4633080
N50 4631220 4633080
Misassemblies
# misassemblies 3 7
Misassembled contigs length 4631220 4633080
Mismatches
# mismatches per 100kbp 1.19 1.42
# indels per 100kbp 1.13 0.83
# N's per 100kbp 533.22 1545.02
Genome statistics
Genome fraction (%) 99.345 98.343
Duplication ratio 1.012 1.016
# genes 4465 + 11 part  4395 + 31 part
NGA50 3180483 687701
Running Time 28m 2hr 01m

Misassemblies for Adobe reader.