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Table 1 Comparison of methods applied to two metagenomic data sets

From: Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

  This work MG-RAST MEGAN AMPHORA 16S rRNA
Average % reads ID’d as bacteria 46 49 63 0.3  
Average % bacterial ID’d as actinobacteria 36.9 49.2 42.6 45.1 28.4
Difference (CREO2 -1) −2.6 −3.6 −3.5 −2.2 −5.1
Average % bacterial ID’d as α-proteobacteria 10.4 20.8 15.1 35.1 29.4
Difference (CREO2 -1) +0.5 +0.9 +0.7 +1.1 +4.0
Average % ID’d as cyanobacteria 0.9 2.6 1.6 0.5 4.0
Difference (CREO2 - 1) −0.6 −0.8 −0.9 −0.8 −2
  1. Selected populations and their changes with field replicates from the desert creosote site (CREO1 and CREO2) are shown. An average of 448k unique reads with an average read length of 375 base pairs was analyzed per sample. Default BLAST E-value cutoffs of 10-3 for MEGAN, and 10-5 for AMPHORA were used. For MG-RAST (v2) we used a E-value cutoff of 10-10, tighter than the default, because it resulted in a similar fraction of reads being assigned. Normalization and definitions of unique reads differ somewhat among methods.