Help pages for anvi'o programs and artifacts

Here you will find a list of all anvi’o programs and artifacts that enable constructing workflows for integrated multi ‘omics investigations.

If you need an introduction to the terminology used in ‘omics research or in anvi’o, please take a look at our vocabulary page. The anvi’o community is with you! If you have practical, technical, or science questions this page to learn about resources available to you. If you are feeling overwhelmed, you can always scream towards the anvi’o

The help contents were last updated on 27 Sep 23 12:58:43 for anvi’o version 8 (marie).

The latest version of anvi’o is v8. See the release notes.

Anvi’o workflows

Anvi’o workflows are dynamic recipes for easy-to-use, scalable, and reproducible bioinformatics analyses through orchestrated use of anvi’o programs as well as third-party software. These workflows typically start with raw data files and a workflow-config and produce anvi’o artifacts, which enable you to outsource rudimentary and relatively well-understood initial steps of your ‘omics analyses so you can focus on more critical downstream research questions by further analyzing these data products inside or outside of the anvi’o software ecosystem.

The anvi’o 8 (marie) contains 5 workflows:

• The anvi'o contigs workflow by
  
  
  
  
  | From FASTA files to annotated anvi'o contigs databases.
• The anvi'o metagenomics workflow by
  
  | From FASTA and/or FASTQ files to anvi'o contigs and profile databases.
• The anvi'o ecophylo workflow by
  
  | Co-characterize the biogeography and phylogeny of any protein.
• The anvi'o trnaseq workflow by
  
  | Process transfer RNA transcripts from tRNA-seq datasets.
• The anvi'o sra-download workflow by
  
  | Download, extract, and gzip paired-end FASTQ files automatically from the NCBI short-read archive (SRA).

Anvi’o artifacts

Anvi’o artifacts represent concepts, file types, or data types anvi’o programs can work with. A given anvi’o artifact can be provided by the user (such as a FASTA file), produced by anvi’o (such as a profile database), or both (such as phylogenomic trees). Anvi’o artifacts link anvi’o programs to each other to build novel workflows.

Listed below a total of 132 artifacts.

	pan-db contigs-db trnaseq-db trnaseq-contigs-db trnaseq-profile-db modules-db structure-db pdb-db kegg-data user-modules-data reaction-ref-data single-profile-db profile-db genes-db genomes-storage-db
	fasta contigs-fasta trnaseq-fasta concatenated-gene-alignment-fasta short-reads-fasta genes-fasta locus-fasta
	dna-sequence
	configuration-ini external-gene-calls external-structures bam-stats-txt bams-and-profiles-txt markdown-txt protein-structure-txt samples-txt primers-txt fasta-txt collection-txt misc-data-items-txt misc-data-layers-txt misc-data-nucleotides-txt misc-data-amino-acids-txt misc-data-layer-orders-txt misc-data-items-order-txt linkmers-txt palindromes-txt inversions-txt gene-calls-txt binding-frequencies-txt functions-txt functional-enrichment-txt functions-across-genomes-txt hmm-hits-across-genomes-txt view-data layer-taxonomy-txt gene-taxonomy-txt genome-taxonomy-txt external-genomes internal-genomes metagenomes hmm-list coverages-txt detection-txt variability-profile-txt codon-frequencies-txt aa-frequencies-txt fixation-index-matrix trnaseq-seed-txt seeds-specific-txt seeds-non-specific-txt modifications-txt quick-summary kegg-metabolism user-metabolism augustus-gene-calls vcf blast-table splits-txt genbank-file groups-txt splits-taxonomy-txt clustering-configuration enzymes-txt enzymes-list-for-module
	paired-end-fastq
	bam-file raw-bam-file
	contigs-stats genes-stats
	svg
	bin
	collection
	hmm-source
	hmm-hits completion misc-data-items misc-data-layers misc-data-nucleotides misc-data-amino-acids genome-similarity misc-data-layer-orders misc-data-items-order metapangenome oligotypes functions kegg-functions reaction-network layer-taxonomy gene-taxonomy genome-taxonomy scgs-taxonomy-db scgs-taxonomy trna-taxonomy-db trna-taxonomy variability-profile split-bins state ngrams pn-ps-data metabolic-independence-score
	cogs-data pfams-data cazyme-data interacdome-data
	dendrogram phylogeny
	reaction-network-json state-json workflow-config
	interactive trnaseq-plot contig-inspection gene-cluster-inspection
	variability-profile-xml
	summary
	workflow

Anvi’o programs

Anvi’o programs perform atomic tasks that can be weaved together to implement complete ‘omics workflows. Please note that there may be programs that are not listed on this page. You can type ‘anvi-‘ in your terminal, and press the TAB key twice to see the full list of programs available to you on your system, and type anvi-program-name --help to read the full list of command line options.

Listed below a total of 147 programs.