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 |  |