Metadata-Version: 2.4
Name: q2-annotate
Version: 2026.7.0.dev0
Summary: QIIME 2 plugin for metagenome analysis.
Author-email: "Michal Ziemski, Keegan Evans" <ziemski.michal@gmail.com>
License: BSD 3-Clause License
        
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Project-URL: Homepage, https://github.com/bokulich-lab/q2-annotate
Project-URL: Repository, https://github.com/bokulich-lab/q2-annotate
Description-Content-Type: text/markdown
License-File: LICENSE
Dynamic: license-file

# q2-annotate
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QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.

## Installation
_q2-annotate_ is available as part of the QIIME 2 moshpit distribution. For installation and usage instructions please consult the official [QIIME 2 documentation](https://docs.qiime2.org).

## Functionality
This QIIME 2 plugin contains actions used to annotate and classify (meta)genomes:

| Action                    | Description                                                                            | Underlying tool       |
|---------------------------|----------------------------------------------------------------------------------------|-----------------------|
| bin-contigs-metabat       | Bin contigs into MAGs using MetaBat 2.                                                 | [MetaBat 2](https://bitbucket.org/berkeleylab/metabat/src/master/) |
| build-custom-diamond-db   | Create a DIAMOND reference database from a FASTA input file.                           | [Diamond](https://github.com/bbuchfink/diamond) |
| build-eggnog-diamond-db   | Create a DIAMOND reference database for the specified taxon.                           | [Diamond](https://github.com/bbuchfink/diamond) |
| build-kraken-db           | Fetch an existing or build a custom Kraken 2 database.                                 | [Kraken 2](https://ccb.jhu.edu/software/kraken2/)      |
| classify-kaiju            | Classify reads using Kaiju.                                                            | [Kaiju](https://bioinformatics-centre.github.io/kaiju/) |
| classify-kraken2          | Classify reads/MAGs using Kraken 2.                                                    | [Kraken 2](https://ccb.jhu.edu/software/kraken2/)      |
| construct-pangenome-index | Construct the human pangenome Bowtie 2 index.                                          | [Bowtie 2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml) |
| dereplicate-mags          | Dereplicate MAGs from multiple samples.                                                | - |
| estimate-abundance        | Estimate contig/MAG abundance.                                                         | - |
| estimate-bracken          | Perform read abundance re-estimation using Bracken.                                    | [Kraken 2](https://ccb.jhu.edu/software/bracken/) |
| evaluate-busco            | Evaluate quality of the generated MAGs using BUSCO.                                    | [BUSCO](https://busco.ezlab.org) |
| extract-annotations       | Extract annotation frequencies from all annotations.                                   | - |
| fetch-busco-db            | Download BUSCO database.                                                               | [BUSCO](https://busco.ezlab.org) |
| fetch-diamond-db          | Fetch the complete Diamond database necessary to run the eggnog-diamond-search action. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| fetch-eggnog-db           | Fetch the databases necessary to run the eggnog-annotate action.                       | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| fetch-eggnog-hmmer-db     | Fetch the taxon specific database necessary to run the eggnog-hmmer-search action.     | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| fetch-eggnog-proteins     | Fetch the databases necessary to run the build-eggnog-diamond-db action.               | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| fetch-kaiju-db            | Fetch Kaiju database.                                                                  | [Kaiju](https://bioinformatics-centre.github.io/kaiju/) |
| fetch-ncbi-taxonomy       | Fetch NCBI reference taxonomy.                                                         | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| filter-derep-mags         | Filter dereplicated MAGs.                                                              | - |
| filter-kraken2-results    | Filter Kraken 2 reports and outputs by metadata and/or abundance                       | - |
| filter-mags               | Filter MAGs.                                                                           | - |
| filter-reads-pangenome    | Remove contaminating human reads.                                                      | [Bowtie 2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml) |
| get-feature-lengths       | Get feature lengths.                                                                   | - |
| inspect-kraken2-db        | Inspect a Kraken 2 database.                                                           | - |
| kraken2-to-features       | Select downstream features from Kraken 2.                                              | - |
| kraken2-to-mag-features   | Select downstream MAG features from Kraken 2.                                          | - |
| map-eggnog                | Annotate orthologs against eggNOG database.                                            | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| multiply-tables           | Multiply two feature tables.                                                           | - |
| predict-genes-prodigal    | Predict gene sequences from MAGs using Prodigal.                                       | [Prodigal](https://github.com/hyattpd/Prodigal) |
| search-orthologs-diamond  | Run eggNOG search using Diamond aligner.                                               | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| search-orthologs-hmmer    | Run eggNOG search using HMMER aligner.                                                 | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
