Metadata-Version: 2.2
Name: q2-annotate
Version: 2025.4.0.dev0+17.g39373a2
Summary: QIIME 2 plugin for metagenome analysis.
Author-email: "Michal Ziemski, Keegan Evans" <ziemski.michal@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2022-2023, QIIME 2 development team.
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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

# q2-annotate
![CI](https://github.com/bokulich-lab/q2-annotate/actions/workflows/ci.yaml/badge.svg)
[![codecov](https://codecov.io/gh/bokulich-lab/q2-annotate/graph/badge.svg?token=PSCAYJUP01)](https://codecov.io/gh/bokulich-lab/q2-annotate)

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/)                  |
| dereplicate-mags                    | Dereplicate MAGs from multiple samples.                                                | - |
| map-eggnog                          | Annotate orthologs against eggNOG database.                                            | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) |
| 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) |
| estimate-bracken                    | Perform read abundance re-estimation using Bracken.                                    | [Kraken 2](https://ccb.jhu.edu/software/bracken/) |
| estimate-mag-abundance              | Estimate MAG abundance.                                                                | - |
| 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-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.                                          | - |
| multiply-tables                     | Multiply two feature tables.                                                           | - |
| predict-genes-prodigal              | Predict gene sequences from MAGs using Prodigal.                                       | [Prodigal](https://github.com/hyattpd/Prodigal) |
