S. aureu

Staphylococcus aureus strain MW2. The S. aureu MW2 consists of a circular chromosome of 2.82 Mb and a plasmid of 20.7 kb in length, respectively.


Read source

The sequence reads were from the supplemental data (supp data) of David Hernandez et al.'s publication (Genome Research 2008). The data set is made up of 3.86 million of 35-bp reads.

Sequence assembly

Software Version Parameters Download
ABySS 1.3.0 k=23 Abyss
Velvet 1.1.04 k=23 min_contig_lgth=100 scaffolding=no Velvet
Edena 3 m=21 Edena
SOAPdenovo 1.05 K=23 M=3 SOAPdenovo

Merged File: S_Contigs

Contig integrator

Integrator Download
CISA CISA
minimus2 minimus2

Evaluation

  • Benchmark genome
Staphylococcus aureus strain MW2
  • Evaluate by Mauve Assembly Metrics
How to score genome assemblies using the Mauve system
  • Score with Mauve metrics:
Name NumContigs NumAssemblyBases DCJ_Distance NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed %Missed ExtraBases %Extra BrokenCDS IntactCDS ContigN50 ContigN90 MaxContigLength Blast_IntactCDS
Velvet 1152 2775301 1124 49 0 1010 866 89319 3.1438 15087 0.5436 230 2421 5337 1329 22892 2265
ABySS 929 2769174 898 41 0 796 601 95493 3.3611 8641 0.312 171 2480 7793 1635 32717 2364
Edena 931 2757686 882 9 0 705 711 99275 3.4942 6966 0.2526 188 2463 6962 1672 37100 2331
SOAPdenovo 944 2781524 917 47 0 853 597 79607 2.802 11796 0.4241 166 2485 6386 1614 26967 2371
CISA 665 2776133 635 48 0 571 388 79805 2.8089 5675 0.2044 100 2551 10533 2460 42008 2463
Minimus2(EVAS) 569 2769617 559 71 0 531 402 85573 3.012 7624 0.2753 107 2544 10672 2578 42022 2468