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Table 2 Defaults for each of the reviewed pipelines

From: A review of software for analyzing molecular sequences

  Mothur QIIME WATERS RDPipeline VAMPS Genboree SnoWMAn
Minimum reads 0 – User defined 200 bp 500 bp 150 bp 200 bp 0 – User defined 150 bp
Maximum reads Not bounded – User defined 1000 bp   500 bp 1000 bp Not bounded – User defined  
Max homopolymers Not bounded – User defined 6 bp      
Number of allowable ambiguous bases (AB) or N’s Not bounded - User defined (recommended AB = 0) AB = 6   N = 0 N = 0 Not bounded – User defined N = 0
Minimum quality score 0 – User defined 25   20   0 – User defined 20
Alignment method Needleman Pynast Infernal Infernal GAST Pynast Varies by pipeline method
Chimera User defined User defined Mallard Uchime   ChimeraSlayer  
  1. bp = base pairs.