S. aure

Revision as of 15 December 2011 19:53 by admin (Comments | Contribs)

Staphylococcus aureus strain MW2

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
  • Scored with Mauve metrics:
Name NumContigs NumAssemblyBases NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed PercBasesMissed ExtraBases PercExtraBases BrokenCDS IntactCDS ContigN50 ContigN90 MaxContigLength
Velvet 1152 2775301 49 0 1010 866 89319 3.1438 15087 0.5436 230 2421 5337 1329 22892
ABySS 929 2769174 41 0 796 601 95493 3.3611 8641 0.312 171 2480 7793 1635 32717
Edena 931 2757686 9 0 705 711 99275 3.4942 6966 0.2526 188 2463 6962 1672 37100
SOAP 944 2781524 47 0 853 597 79607 2.802 11796 0.4241 166 2485 6386 1614 26967
CISA 692 2782831 46 0 596 415 80370 2.8288 12281 0.4413 106 2545 10284 2356 42008
Minimus2 569 2769617 71 0 531 402 85573 3.012 7624 0.2753 107 2544 10672 2578 42022