Anvio

Introduction

Anvio is an analysis and visualization platform for ‘omics data.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/anvio
Home page: https://github.com/merenlab/anvio

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

7.0, 7.1_main, 7.1_structure

BELL

7.0, 7.1_main, 7.1_structure

GAUTSCHI

7.0, 7.1_main, 7.1_structure

NEGISHI

7.0, 7.1_main, 7.1_structure

SCHOLAR

7.0, 7.1_main, 7.1_structure

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 clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers anvio

# Your anvio workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers anvio

# Your anvio workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers anvio

# Your anvio workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers anvio

# Your anvio workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers anvio

# Your anvio workflow...