TABLE 1.
Comparison of targeted assembler software for SSU rRNA sequences
| Tool | Read extraction |
Database | Method | Taxon classifier |
Availability | Documentation | License | Last release (yr-mo-day)a |
|---|---|---|---|---|---|---|---|---|
| Emirge | Bowtie (v1) | SILVA | Expectation maximization |
(From mapping) |
GitHub, Conda |
Readme, user forum |
GPL3 | v0.61.1 2016-12-03 |
| REAGO | Infernal (CM) | NA | Overlap graph, pruning, paired-end guided path-finding |
NA | GitHub, Conda |
Readme | BSD | v1.1 2015-12-18 |
| Matam | SortMeRNA | SILVA NR95 | Overlap graph, compression, SGA assembler on subgraphs |
RDP classifier |
GitHub, Conda, Docker |
Readme | AGPL3 | v1.6.0 2019-10-09 |
| RAMBL | Bowtie2 | Greengenes | Taxonomic tree search and Dirichlet process clustering |
RDP classifier |
GitHub | Readme | Not specified | NA last commit 2017-03-18 |
a
As of 1 October 2020. NA, not available.