All tools are accessible as Apps in the CyVerse Discovery Environment (formerly iPlant). The CyVerse Cyberinfrastructure is a freely available resource for computation, storage, and data analysis for the life sciences. We plan to extend the list of tools for viruses pending funding.  The are also general Apps for metagenomics and microbial ecology available through the iMicrobe Project.

Clicking on tools will take you to the App on CyVerse!

iMicrobe/iVirus Tools

Quality Control
Name Description
Trimmomatic Identifies adapter sequences and quality filters
Btrim Trims adapters and low quality regions
Scythe Identifies contaminating sequences in read data based on a Bayesian approach
Sickle Sliding window quality trimmer, designed to be used after Scythe
Gene Calling
Name Description
MetaGeneMark Ab initio gene prediction
FragGeneScan Ab initio gene prediction
Prodigal Ab initio gene prediction
Assemblers
Name Description
SOAPDenovo Single-genome assembler tuned for metagenomics
Newbler (gs Assembler) De novo assembly based on read overlap
SPAdes (multiple memory) De Bruijn graph assembler
IDBA-UD (multiple memory) De Bruijn graph multiple alignments
Viral Analysis
Name Description
PCPipe Protein clustering pipeline and annotation
VirSorter Find viral contigs in a microbial metagenome
vContact Guilt-by-contig-association automatic classification of viral contigs
vContact-PCs Generate PC-profiles using vContact/MCL
vContact-Gene2Contig Conditions files for use in vContact
GAAS (Genome Abundance and Average Size) (In development) Estimates relative abundance and average size of metagenomic sequences
Circonspect (In development) Generates contig spectra for downstream modeling of community structure
PHACCS (Control In Research on CONtig SPECTra) (In development) Estimates structure and diversity of viral communities
BatchBowtie Performs mass alignment of paired and unpaired reads against a reference dataset using Bowtie2 and Samtools.
Read2RefMapper Filters read coverage (BAM files from alignments like Bowtie2) against a reference dataset and generates relative abundance tables

iVirus tool updates (both improvements and bugs) will be worked on pending funding and time availability.