Table 1 Comparison of read-based metagenomic annotation pipeline features
Feature | MG-RAST | SUPER-FOCUS | eggNOG-mapper | HUMAnN2 | YAMP | MetaLAFFA |
|---|---|---|---|---|---|---|
Metagenomic functional annotation | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Uses DIAMOND for read alignment | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Read pre-processing | ✓ | ✓ | ✓ | |||
Ortholog aggregation to broader functional categorizations | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Available as a web service | ✓ | ✓ | ||||
Native integration with distributed computing systems | ✓ | ✓ | ||||
Automatic continuation from intermediate steps after interruption | ✓ | ✓ | ✓ | |||
Convenient incorporation of new pipeline steps | ✓ | ✓ | ||||
Universal single-copy gene-based abundance normalization via MUSiCC | ✓ |