Skip to main content

Table 1 Feature comparison for metagenomic pipelines

From: Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

  Sunbeam SURPI KneadData EDGE ATLAS
Architecture/usage
 Dependency management Conda Bash Pip (partial)   Conda
 Modularity Snakemake    Perl modules Snakemake
 Results reporting Tables, coverage maps, figures Tables, coverage maps    Tables, coverage maps
 Extension framework Sunbeam extensions     
 Clinical certification   CLIA    
 Data source Local, SRA Local Local Local Local
Quality control
 Adapter trimming Trimmomatic, Cutadapt Cutadapt Trimmomatic FaQCs BBDuk2
 Error correction      Tadpole
 Read quality Fastqc Cutadapt Fastqc FaQCs BBDuk2
 Host filtering Any Human Any Any Any
 Low complexity Komplexity DUST TRF Mono- or dinucleotide repeats BBDuk2
 Read subsampling/rarefaction VSEARCH (extension)     
Sequence analysis
 Reference alignment BWA    Bowtie2, MUMmer + JBrowse BBMap
 Classification Kraken, (MetaPhlAn2, Kaiju extensions) SNAP   GOTTCHA, Kraken, MetaPhlAn DIAMOND
 Assembly MEGAHIT Minimo   IDBA-UD, SPAdes MEGAHIT, SPAdes
 ORFs (aa) Prodigal, BLASTp     Prokka
 Full contig (nt) Circularity, BLASTn RAPSearch   BWA DIAMOND
 Functional annotation eggNOG (extension)     ENZYME/eggNOG/ dbCAN
 Phylogeny reconstruction     PhaMe, FastTree/RAxML  
 Primer design     BW, Primer3  
  1. Feature comparison for metagenomic pipelines. Tools used by each pipeline: trimmomatic [46], cutadapt [45], tadpole [78], fastqc [47], FaQCs [79], BBDuk2 [80], DUST [36], TRF [81], VSEARCH [82], bwa [48], bowtie2 [83], BBMap [84], KRAKEN [49], SNAP [85], MUMmer [86], JBrowse [87], GOTTCHA [88], MetaPhlAn [58], DIAMOND [89], FastTree [90], MEGAHIT [51], SPAdes [91], Minimo [92], Prodigal [52], BLASTp [53], Prokka [93], BLASTn [53], eggNOG [94], ENZYME [95], dbCAN [96], Primer3 [97], RAPSearch [98], RAxML [99], conda [43], PhaME [100], Snakemake [30], SAMtools [54]