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Table 3 Top-five assemblies for each case study shown in this work with their respective mean distances from references (MD)

From: TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms

Assembly ID Module 1 Module 2 Module 3 MD
Case study 1: Grapevine
 scOasesK35
  OASES-scaffolded assembly with k-mer 35    0.383
 scOasesK25
  OASES-scaffolded assembly with k-mer 25    0.890
 scSoap_cat_cd_rcMin2
  Concatenation of the two SOAP-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation    1.179
 scOases_cat
  Concatenation of the two SOAP-scaffolded assemblies with different kmers    1.249
 scRay_cat_cd_rcMin2
  Concatenation of the two RAY-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation    1.311
Case study 2: Olive tree
 scOases_cat_cd
  Concatenation of the two OASES-scaffolded assemblies with different kmers and sequence redundancy removal    0.297
 aaMin2/scALL/454Cap3
  All scafolded assemblies CAP3-reconciled assembly Minimus2-combined assembly of assemblies 0.323
 scOases_cat
  Concatenation of the two SOAP-scaffolded assemblies with different kmers    0.324
 arMIRA/scOases_cat_cd
  Concatenation of the two OASES-scaffolded assemblies with different kmers and sequence redundancy removal Pre-processed reads Assembly-reads combination using MIRA4 0.352
 aaMin2/scOases_cat_cd_rcMin2/454Cap3
  Concatenation of the two OASES-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation CAP3-reconciled assembly Minimus2-combined assembly of assemblies 0.367
Case study 3: Chestnut
 arMIRA/scOases_cat_cd_rcMin2
  Concatenation of the two OASES-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation Pre-processed reads Assembly-reads combination using MIRA4 0.189
 arMIRA/scOases_cat_cd
  Concatenation of the two OASES-scaffolded assemblies with different kmers and sequence redundancy removal Pre-processed reads Assembly-reads combination using MIRA4 0.205
 arMIRA/scOasesK25
  OASES-scaffolded assembly with k-mer 25 Pre-processed reads Assembly-reads combination using MIRA4 0.225
 aaMin2/scOases_cat_cd_rcMin2/454Cap3
  Concatenation of the two OASES-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation CAP3-reconciled assembly Minimus2-combined assembly of assemblies 0.269
 aaMin2/scALL/454Cap3
  All scafolded assemblies CAP3-reconciled assembly Minimus2-combined assembly of assemblies 0.270
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BMC Bioinformatics

ISSN: 1471-2105

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