Anvio
Introduction
Anvio
is an analysis and visualization platform for ‘omics data.
Versions
7.0
Commands
anvi-analyze-synteny
anvi-cluster-contigs
anvi-compute-ani
anvi-compute-completeness
anvi-compute-functional-enrichment
anvi-compute-gene-cluster-homogeneity
anvi-compute-genome-similarity
anvi-convert-trnaseq-database
anvi-db-info
anvi-delete-collection
anvi-delete-hmms
anvi-delete-misc-data
anvi-delete-state
anvi-dereplicate-genomes
anvi-display-contigs-stats
anvi-display-metabolism
anvi-display-pan
anvi-display-structure
anvi-estimate-genome-completeness
anvi-estimate-genome-taxonomy
anvi-estimate-metabolism
anvi-estimate-scg-taxonomy
anvi-estimate-trna-taxonomy
anvi-experimental-organization
anvi-export-collection
anvi-export-contigs
anvi-export-functions
anvi-export-gene-calls
anvi-export-gene-coverage-and-detection
anvi-export-items-order
anvi-export-locus
anvi-export-misc-data
anvi-export-splits-and-coverages
anvi-export-splits-taxonomy
anvi-export-state
anvi-export-structures
anvi-export-table
anvi-gen-contigs-database
anvi-gen-fixation-index-matrix
anvi-gen-gene-consensus-sequences
anvi-gen-gene-level-stats-databases
anvi-gen-genomes-storage
anvi-gen-network
anvi-gen-phylogenomic-tree
anvi-gen-structure-database
anvi-gen-variability-matrix
anvi-gen-variability-network
anvi-gen-variability-profile
anvi-get-aa-counts
anvi-get-codon-frequencies
anvi-get-enriched-functions-per-pan-group
anvi-get-sequences-for-gene-calls
anvi-get-sequences-for-gene-clusters
anvi-get-sequences-for-hmm-hits
anvi-get-short-reads-from-bam
anvi-get-short-reads-mapping-to-a-gene
anvi-get-split-coverages
anvi-help
anvi-import-collection
anvi-import-functions
anvi-import-items-order
anvi-import-misc-data
anvi-import-state
anvi-import-taxonomy-for-genes
anvi-import-taxonomy-for-layers
anvi-init-bam
anvi-inspect
anvi-interactive
anvi-matrix-to-newick
anvi-mcg-classifier
anvi-merge
anvi-merge-bins
anvi-meta-pan-genome
anvi-migrate
anvi-oligotype-linkmers
anvi-pan-genome
anvi-profile
anvi-push
anvi-refine
anvi-rename-bins
anvi-report-linkmers
anvi-run-hmms
anvi-run-interacdome
anvi-run-kegg-kofams
anvi-run-ncbi-cogs
anvi-run-pfams
anvi-run-scg-taxonomy
anvi-run-trna-taxonomy
anvi-run-workflow
anvi-scan-trnas
anvi-script-add-default-collection
anvi-script-augustus-output-to-external-gene-calls
anvi-script-calculate-pn-ps-ratio
anvi-script-checkm-tree-to-interactive
anvi-script-compute-ani-for-fasta
anvi-script-enrichment-stats
anvi-script-estimate-genome-size
anvi-script-filter-fasta-by-blast
anvi-script-fix-homopolymer-indels
anvi-script-gen-CPR-classifier
anvi-script-gen-distribution-of-genes-in-a-bin
anvi-script-gen-help-pages
anvi-script-gen-hmm-hits-matrix-across-genomes
anvi-script-gen-programs-network
anvi-script-gen-programs-vignette
anvi-script-gen-pseudo-paired-reads-from-fastq
anvi-script-gen-scg-domain-classifier
anvi-script-gen-short-reads
anvi-script-gen_stats_for_single_copy_genes.R
anvi-script-gen_stats_for_single_copy_genes.py
anvi-script-gen_stats_for_single_copy_genes.sh
anvi-script-get-collection-info
anvi-script-get-coverage-from-bam
anvi-script-get-hmm-hits-per-gene-call
anvi-script-get-primer-matches
anvi-script-merge-collections
anvi-script-pfam-accessions-to-hmms-directory
anvi-script-predict-CPR-genomes
anvi-script-process-genbank
anvi-script-process-genbank-metadata
anvi-script-reformat-fasta
anvi-script-run-eggnog-mapper
anvi-script-snvs-to-interactive
anvi-script-tabulate
anvi-script-transpose-matrix
anvi-script-variability-to-vcf
anvi-script-visualize-split-coverages
anvi-search-functions
anvi-self-test
anvi-setup-interacdome
anvi-setup-kegg-kofams
anvi-setup-ncbi-cogs
anvi-setup-pdb-database
anvi-setup-pfams
anvi-setup-scg-taxonomy
anvi-setup-trna-taxonomy
anvi-show-collections-and-bins
anvi-show-misc-data
anvi-split
anvi-summarize
anvi-trnaseq
anvi-update-db-description
anvi-update-structure-database
anvi-upgrade
Module
You can load the modules by:
module load biocontainers
module load anvio
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run Anvio on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=anvio
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers anvio
anvi-script-reformat-fasta assembly.fa -o contigs.fa -l 1000 --simplify-names --seq-type NT
anvi-gen-contigs-database -f contigs.fa -o contigs.db -n 'An example contigs database' --num-threads 8
anvi-display-contigs-stats contigs.db
anvi-setup-ncbi-cogs --cog-data-dir $PWD --num-threads 8 --just-do-it --reset
anvi-run-ncbi-cogs -c contigs.db --cog-data-dir COG20 --num-threads 8