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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]