Ecoli

Revision as of 07 December 2011 01:15 by admin (Comments | Contribs)

Eshcherichia coli K12 MG1655

Read source

The illuminia read data of E coli (Paired-end sequencing library with 200 bp inserts) downloaded from Sequence Read Archive (SRA).

Sequence assembly

  • Set1 (Different Assemblers)
Software Version Parameters Download
ABySS 1.3.0 k=31 Abyss
Velvet 1.1.04 k=29 ins_length=215 cov_cutoff=12 exp_cov=24 min_contig_lgth=100 scaffolding=no Velvet
Edena 3 m=30 Edena
SOAPdenovo 1.05 K=29 M=3 SOAPdenovo
CLC 4.7.2 insert_size_range=194,236 minimum_contig_length=100 CLC

Merged File: Set1_Contig

  • Set2 (Different parameters for Abyss - the assembler provides the lowest number of contigs in Set1)
Abyss parameter Download
k=29 Abyss_k29
k=31 Abyss_k31
k=33 Abyss_k33

Merged File: Set2_Contig

  • Set3 (Different parameters for SOAPdenovo - the assembler provides the largest number of contigs in Set1)
SOAPdenovo parameter Download
k=29 SOAP_k29
k=31 SOAP_k31
k=33 SOAP_k33

Merged File: Set3_Contig

Contig integrator

  • CISA
Input Download
Set1 CISA_Set1
Set2 CISA_Set2
Set3 CISA_Set3
Set2+Set3 CISA_Set2&3
  • minimus2
Input Download
Set1 minimus2_Set1

Evaluation

  • Benchmark genome
Eshcherichia coli K12 MG1655
  • Evaluate by Mauve Assembly Metrics
How to score genome assemblies using the Mauve system
  • Set1
Name NumContigs NumAssemblyBases NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed PercBasesMissed ExtraBases PercExtraBases BrokenCDS IntactCDS ContigN50 ContigN90 MinContigLength MaxContigLength
CISA_Set1 81 4625471 229 73 92 93 54849 1.1822 32166 0.6954 46 4274 113510 29195 109 268608
minimus2 74 4608653 285 0 97 78 76881 1.657 35464 0.7695 50 4270 126075 34542 180 417704
Abyss 133 4626205 334 69 123 119 57847 1.2468 29424 0.636 57 4263 96157 26096 100 222425
CLC 379 4546926 100 0 288 287 130550 2.8138 3405 0.0749 62 4258 29767 8447 99 107342
Edena 211 4569446 17 0 129 125 86780 1.8704 2078 0.0455 66 4254 54405 13642 100 186686
SOAPdenovo 553 4547211 36 0 461 412 124407 2.6814 6972 0.1533 100 4220 17902 5384 100 103369
Velvet 283 4550675 138 0 208 203 116542 2.5119 2783 0.0612 74 4246 52474 12537 100 166094