E. coli 100 bp

Revision as of 08 September 2012 01:27 by admin (Comments | Contribs)

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)

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
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