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