An anvi’o genomes storage is a special database that stores information about genomes. A genomes storage can be generated only from external genomes, only from internal genomes, or it can contain both types. Before we go any further, here are some definitions to clarify things:
An external genome is anything you have in a FASTA file format (i.e., a genome you have downloaded from NCBI, or obtained through any other way).
An internal genome is any genome bin you stored in an anvi’o collection at the end of your metagenomic analysis (if you are not familiar with the anvi’o metagenomic workflow please take a look at this post).
Converting FASTA files into anvi’o contigs databases: Working with internal genomes is quite straightforward since you already have an anvi’o contigs and an anvi’o profile database for them. But if all you have is a bunch of FASTA files, this workflow will require you to convert each of them into an anvi’o contigs database. There is a lot of information about how to create an anvi’o contigs database here, but if you feel lazy, you can also use the script anvi-script-FASTA-to-contigs-db
, which requires a single parameter: the FASTA file path. Power users should consider taking a look at the code, and create their own batch script with improvements on those lines based on their needs (for instance, increasing the number of threads when running HMMs, etc). Also, you may want to run anvi-run-ncbi-cogs
on your contigs database to annotate your genes.
You can create a new anvi’o genomes storage using the program anvi-gen-genomes-storage
, which will require you to provide descriptions of genomes to be included in this storage. File formats for external genome and internal genome descriptions differ slightly. For instance, this is an example --external-genomes
file:
name | contigs_db_path |
---|---|
Name_01 | /path/to/contigs-01.db |
Name_02 | /path/to/contigs-02.db |
Name_03 | /path/to/contigs-03.db |
(…) | (…) |
and this is an example file for --internal-genomes
:
name | bin_id | collection_id | profile_db_path | contigs_db_path |
---|---|---|---|---|
Name_01 | Bin_id_01 | Collection_A | /path/to/profile.db | /path/to/contigs.db |
Name_02 | Bin_id_02 | Collection_A | /path/to/profile.db | /path/to/contigs.db |
Name_03 | Bin_id_03 | Collection_B | /path/to/another_profile.db | /path/to/another/contigs.db |
(…) | (…) | (…) | (…) | (…) |
For names in the first column please use only letters, digits, and the underscore character.
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Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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do
anvi-script-FASTA-to-contigs-db $i
--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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{"fasta_txt": "fasta.txt","anvi_run_scg_taxonomy": {"run": false},"anvi_run_scg_taxonomy": {"run": false},"output_dirs": {"FASTA_DIR": "01_FASTA_contigs_workflow","CONTIGS_DIR": "02_CONTIGS_contigs_workflow","LOGS_DIR": "00_LOGS_contigs_workflow"}}
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--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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