Table 1 Major functions of seven pipelines
From: A review of software for analyzing molecular sequences
Capabilities | Mothur | Qiime | Waters | RD-Pipline | VAMPS‡ | Genboree‡ | SnoWMAn‡ | |
|---|---|---|---|---|---|---|---|---|
Documentation | Available guides | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Installation | Shortcut option (instant download) | ✓ | ✓ | |||||
Native version: Mac OSX | ✓ | ✓ | ✓†| |||||
Native version: Windows | ✓ | ✓ | ✓ | |||||
Native version: Linux | ✓ | ✓ | ✓ | |||||
Web based | ✓ | ✓ | ✓ | ✓ | ||||
Updating | Re-download entire program | ✓ | ✓ | ✓ | ||||
Re-download updated sections | ✓ | |||||||
Interface | Command line | ✓ | ✓ | |||||
Graphical User Interface | ✓ | |||||||
Web form GUI | ✓ | ✓ | ✓ | ✓ | ||||
Sequencing platforms | Illumina | ✓ | ✓ | ✓ | ✓†| ✓ | ✓ | ✓ |
454 Pyroseq | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓†| |
Preparing sequences | Accepted file formats | |||||||
sff | ✓* | ✓* | ✓ | ✓ | ✓ | |||
Fasta | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Quality score | ✓ | ✓ | ✓ | ✓ | ||||
Flow file data | ✓ | ✓ | ||||||
User defined barcodes or primers | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
User defined metadata | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Alignment | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Summary function | ✓ | ✓ | ✓ | |||||
Trims barcodes and primers off of sequences | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Removes short reads | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Identify and remove chimeras | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Remove contaminants | ✓ | ✓ | ||||||
Approaches to analyze files | OTU binning/clustering | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Phylotype binning | ✓ | ✓ | ✓ | |||||
Phylogenetic tree | ✓ | ✓ | ✓ | ✓ | ||||
Analysis output | Alpha diversity | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Beta diversity | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Ecological indexes | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Unifrac | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Visualization | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |