Ecoli

Revision as of 07 December 2011 01:13 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 NumReferenceBases NumLCBs DCJ_Distance NumDCJBlocks NumSNPs NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed PercBasesMissed ExtraBases PercExtraBases BrokenCDS IntactCDS ContigN50 ContigN90 MinContigLength MaxContigLength
CISA_Set1 81 4625471 4639675 2 74 75 302 229 73 92 93 54849 1.1822 32166 0.6954 46 4274 113510 29195 109 268608
minimus2 74 4608653 4639675 5 67 68 285 285 0 97 78 76881 1.657 35464 0.7695 50 4270 126075 34542 180 417704
Abyss 133 4626205 4639675 2 107 108 403 334 69 123 119 57847 1.2468 29424 0.636 57 4263 96157 26096 100 222425
CLC 379 4546926 4639675 5 303 304 100 100 0 288 287 130550 2.8138 3405 0.0749 62 4258 29767 8447 99 107342
Edena 211 4569446 4639675 2 153 154 17 17 0 129 125 86780 1.8704 2078 0.0455 66 4254 54405 13642 100 186686
SOAPdenovo 553 4547211 4639675 2 474 475 36 36 0 461 412 124407 2.6814 6972 0.1533 100 4220 17902 5384 100 103369
Velvet 283 4550675 4639675 2 206 207 138 138 0 208 203 116542 2.5119 2783 0.0612 74 4246 52474 12537 100 166094