All tools are accessible as Apps in the iPlant Discovery Environment. The iPlant Cyberinfrastructure is a freely available resource for computation, storage, and data analysis for the life sciences. We plan to extend the list of tools pending funding.
Assemblers
| Name | Description |
|---|---|
| ABySS | De novo sequence assembly |
| ALLPATHS-LG | De novo sequence assembly |
| khmer | Probabilistic de Bruijn graphs |
| Meta-IDBA | De Bruijn graph multiple alignments |
| MetaVelvet | De Bruijn graph coverage and connectivity |
| Newbler | De novo assembly based on read overlap |
| SOAPdenovo | Single-genome assembler tuned for metagenomics |
| SPA | Short peptide assembly for metagenomes |
| Velvet | De Bruijn graph coverage and connectivity |
Gene Calling
| Name | Description |
|---|---|
| FragGeneScan | Ab initio gene prediction |
| Glimmer | Ab initio gene prediction |
| Prodigal | Ab initio gene prediction |
| Metagene | Ab initio gene prediction |
| MetaGenmark | Ab initio gene prediction |
Viral Analysis Pipelines
| Name | Description |
|---|---|
| PCPipe | Protein clustering pipeline and annotation |
| VirSorter | Find viral contigs in a microbial metagenome |