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Table 4 Top-five assemblies by biological structure for P. xanthii with their respective mean distances from references

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
Haustorium
 scOases_cat_cd_rcMin2
  Concatenation of the two OASES-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation    0.3848
 scOases_cat
  Concatenation of the two OASES-scaffolded assemblies with different kmers    0.3850
 scOases_cat_cd
  Concatenation of the two OASES-scaffolded assemblies with different kmers and sequence redundancy removal    0.3861
 scSoap_cat_cd
  Concatenation of the two SOAP-scaffolded assemblies with different kmers and sequence redundancy removal    0.3887
 scOasesK35
  OASES-scaffolded assembly with k-mer 35    0.3915
Epiphytic structures
 ctMIRA_ctEulK29_rcCAP3
   CAP3-reconciled assembly   0.0558
 ctMIRA
   MIRA4-primary assembly   0.0688
 ctEulK29
   EULER-SR primary assembly with k-mer 29   0.1435
Comprehensive transcriptome
 arMIRA/scSoap_cat_cd_rcMin2
  Concatenation of the two SOAP-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation Pre-processed reads Assembly-reads combination using MIRA4 0.0470
 arMIRA/ctSoapK25
  SOAP-primary assembly with k-mer 25 Pre-processed reads Assembly-reads combination using MIRA4 0.0473
 arMIRA/scRay_cat_cd_rcMin2
  Concatenation of the two RAY-scaffolded assemblies with different kmers, sequence redundancy removal and Minimus2 reconciliation Pre-processed reads Assembly-reads combination using MIRA4 0.0476
 arMIRA/ctRayK35
  RAY-primary assembly with k-mer 35 Pre-processed reads Assembly-reads combination using MIRA4 0.0479
 arMIRA/ctSoap_cat_cd_rcMin2
  Concatenation of the two SOAP-primary assembling kmers, sequence redundancy removal and Minimus2 reconciliation Pre-processed reads Assembly-reads combination using MIRA4 0.0479
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