E. coli 100 bp

Revision as of 08 September 2012 02:03 by admin (Comments | Contribs) | (→Evaluation)

Escherichia coli K12 MG1655. The E. coli MG1655 consists of a circular chromosome of 4,639,675 bp in length.

Read source

The paired-end illuminia read data of E. coli were downloaded from Illumina (|Illumina) with a median insert size of 214 bp. More than 28.4 M reads

Sequence assembly

Software Version Parameters Download
ABySS 1.3.0 k=75 Abyss
Velvet 1.1.04 VelvetOptimiser --s 59 --e 97 Velvet
Edena 3 m=75 Edena
SOAPdenovo 1.05 k=75 M=3 avg_ins=215 SOAPdenovo

Merged File: E100_Contigs

Contig integrator

Integrator Download
CISA CISA
minimus2 minimus2(AEVS),minimus2(ASEV), minimus2(ASVE), minimus2(ESAV),minimus2(ESVA), minimus2(SEAV), minimus2(SEVA), minimus2(SVAE), minimus2(VASE), minimus2(VEAS)
GAA GAA(AESV),GAA(AEVS), GAA(ASEV), GAA(EASV),GAA(EAVS), GAA(ESAV), GAA(EVAS), GAA(EVSA), GAA(VAES), GAA(VASE)

Beacuase minimus2 and GAA merge two assemblies at a time, we iteratively integrate the four assemblies in random order.

Evaluation

  • Benchmark genome
Eshcherichia coli K12 MG1655
  • 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 Units(>200) N50 cor.Units cor.N50 Errors,(Indel>=5,Inv,Rel)
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