q2-annotate

bokulich-lab

Quickstart install for:

[Fresh Install]

[Update Existing]

conda env create --name q2-annotate-metagenome-2024.10 --file https://raw.githubusercontent.com/bokulich-lab/q2-annotate/refs/heads/main/environment-files/q2-annotate-qiime2-metagenome-2024.10.yml

Activate your environment (metagenome-2024.10) and run:

conda env update --file https://raw.githubusercontent.com/bokulich-lab/q2-annotate/refs/heads/main/environment-files/q2-annotate-qiime2-metagenome-2024.10.yml

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.

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
build-custom-diamond-db	Create a DIAMOND reference database from a FASTA input file.	Diamond
build-eggnog-diamond-db	Create a DIAMOND reference database for the specified taxon.	Diamond
build-kraken-db	Fetch an existing or build a custom Kraken 2 database.	Kraken 2
classify-kaiju	Classify reads using Kaiju.	Kaiju
classify-kraken2	Classify reads/MAGs using Kraken 2.	Kraken 2
dereplicate-mags	Dereplicate MAGs from multiple samples.	-
map-eggnog	Annotate orthologs against eggNOG database.	EggNOG mapper
search-orthologs-diamond	Run eggNOG search using Diamond aligner.	EggNOG mapper
search-orthologs-hmmer	Run eggNOG search using HMMER aligner.	EggNOG mapper
estimate-bracken	Perform read abundance re-estimation using Bracken.	Kraken 2
estimate-mag-abundance	Estimate MAG abundance.	-
evaluate-busco	Evaluate quality of the generated MAGs using BUSCO.	BUSCO
extract-annotations	Extract annotation frequencies from all annotations.	-
fetch-busco-db	Download BUSCO database.	BUSCO
fetch-diamond-db	Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.	EggNOG mapper
fetch-eggnog-db	Fetch the databases necessary to run the eggnog-annotate action.	EggNOG mapper
fetch-eggnog-hmmer-db	Fetch the taxon specific database necessary to run the eggnog-hmmer-search action.	EggNOG mapper
fetch-eggnog-proteins	Fetch the databases necessary to run the build-eggnog-diamond-db action.	EggNOG mapper
fetch-kaiju-db	Fetch Kaiju database.	Kaiju
fetch-ncbi-taxonomy	Fetch NCBI reference taxonomy.	EggNOG mapper
filter-derep-mags	Filter dereplicated MAGs.	-
filter-mags	Filter MAGs.	-
filter-reads-pangenome	Remove contaminating human reads.	Bowtie 2
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

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.

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
build-custom-diamond-db	Create a DIAMOND reference database from a FASTA input file.	Diamond
build-eggnog-diamond-db	Create a DIAMOND reference database for the specified taxon.	Diamond
build-kraken-db	Fetch an existing or build a custom Kraken 2 database.	Kraken 2
classify-kaiju	Classify reads using Kaiju.	Kaiju
classify-kraken2	Classify reads/MAGs using Kraken 2.	Kraken 2
dereplicate-mags	Dereplicate MAGs from multiple samples.	-
map-eggnog	Annotate orthologs against eggNOG database.	EggNOG mapper
search-orthologs-diamond	Run eggNOG search using Diamond aligner.	EggNOG mapper
search-orthologs-hmmer	Run eggNOG search using HMMER aligner.	EggNOG mapper
estimate-bracken	Perform read abundance re-estimation using Bracken.	Kraken 2
estimate-mag-abundance	Estimate MAG abundance.	-
evaluate-busco	Evaluate quality of the generated MAGs using BUSCO.	BUSCO
extract-annotations	Extract annotation frequencies from all annotations.	-
fetch-busco-db	Download BUSCO database.	BUSCO
fetch-diamond-db	Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.	EggNOG mapper
fetch-eggnog-db	Fetch the databases necessary to run the eggnog-annotate action.	EggNOG mapper
fetch-eggnog-hmmer-db	Fetch the taxon specific database necessary to run the eggnog-hmmer-search action.	EggNOG mapper
fetch-eggnog-proteins	Fetch the databases necessary to run the build-eggnog-diamond-db action.	EggNOG mapper
fetch-kaiju-db	Fetch Kaiju database.	Kaiju
fetch-ncbi-taxonomy	Fetch NCBI reference taxonomy.	EggNOG mapper
filter-derep-mags	Filter dereplicated MAGs.	-
filter-mags	Filter MAGs.	-
filter-reads-pangenome	Remove contaminating human reads.	Bowtie 2
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

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.

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
build-custom-diamond-db	Create a DIAMOND reference database from a FASTA input file.	Diamond
build-eggnog-diamond-db	Create a DIAMOND reference database for the specified taxon.	Diamond
build-kraken-db	Fetch an existing or build a custom Kraken 2 database.	Kraken 2
classify-kaiju	Classify reads using Kaiju.	Kaiju
classify-kraken2	Classify reads/MAGs using Kraken 2.	Kraken 2
dereplicate-mags	Dereplicate MAGs from multiple samples.	-
map-eggnog	Annotate orthologs against eggNOG database.	EggNOG mapper
search-orthologs-diamond	Run eggNOG search using Diamond aligner.	EggNOG mapper
search-orthologs-hmmer	Run eggNOG search using HMMER aligner.	EggNOG mapper
estimate-bracken	Perform read abundance re-estimation using Bracken.	Kraken 2
estimate-mag-abundance	Estimate MAG abundance.	-
evaluate-busco	Evaluate quality of the generated MAGs using BUSCO.	BUSCO
extract-annotations	Extract annotation frequencies from all annotations.	-
fetch-busco-db	Download BUSCO database.	BUSCO
fetch-diamond-db	Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.	EggNOG mapper
fetch-eggnog-db	Fetch the databases necessary to run the eggnog-annotate action.	EggNOG mapper
fetch-eggnog-hmmer-db	Fetch the taxon specific database necessary to run the eggnog-hmmer-search action.	EggNOG mapper
fetch-eggnog-proteins	Fetch the databases necessary to run the build-eggnog-diamond-db action.	EggNOG mapper
fetch-kaiju-db	Fetch Kaiju database.	Kaiju
fetch-ncbi-taxonomy	Fetch NCBI reference taxonomy.	EggNOG mapper
filter-derep-mags	Filter dereplicated MAGs.	-
filter-mags	Filter MAGs.	-
filter-reads-pangenome	Remove contaminating human reads.	Bowtie 2
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

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.

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
build-custom-diamond-db	Create a DIAMOND reference database from a FASTA input file.	Diamond
build-eggnog-diamond-db	Create a DIAMOND reference database for the specified taxon.	Diamond
build-kraken-db	Fetch an existing or build a custom Kraken 2 database.	Kraken 2
classify-kaiju	Classify reads using Kaiju.	Kaiju
classify-kraken2	Classify reads/MAGs using Kraken 2.	Kraken 2
dereplicate-mags	Dereplicate MAGs from multiple samples.	-
map-eggnog	Annotate orthologs against eggNOG database.	EggNOG mapper
search-orthologs-diamond	Run eggNOG search using Diamond aligner.	EggNOG mapper
search-orthologs-hmmer	Run eggNOG search using HMMER aligner.	EggNOG mapper
estimate-bracken	Perform read abundance re-estimation using Bracken.	Kraken 2
estimate-mag-abundance	Estimate MAG abundance.	-
evaluate-busco	Evaluate quality of the generated MAGs using BUSCO.	BUSCO
extract-annotations	Extract annotation frequencies from all annotations.	-
fetch-busco-db	Download BUSCO database.	BUSCO
fetch-diamond-db	Fetch the complete Diamond database necessary to run the eggnog-diamond-search action.	EggNOG mapper
fetch-eggnog-db	Fetch the databases necessary to run the eggnog-annotate action.	EggNOG mapper
fetch-eggnog-hmmer-db	Fetch the taxon specific database necessary to run the eggnog-hmmer-search action.	EggNOG mapper
fetch-eggnog-proteins	Fetch the databases necessary to run the build-eggnog-diamond-db action.	EggNOG mapper
fetch-kaiju-db	Fetch Kaiju database.	Kaiju
fetch-ncbi-taxonomy	Fetch NCBI reference taxonomy.	EggNOG mapper
filter-derep-mags	Filter dereplicated MAGs.	-
filter-mags	Filter MAGs.	-
filter-reads-pangenome	Remove contaminating human reads.	Bowtie 2
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

Links

Documentation

Source Code

Stars

Last Commit

3cc6b61

Available Distros

2024.10: 2024.10/metagenome