🎬 Actions

Documentation for q2-mosphit Actions

Qiime2 actions are programs that fetch, transform, or analyze data. Keep in mind that normal data files cannot be used as input to actions. Data must be in the form of artifacts. Read more about artifacts and semantic types in the Semantic Types page or in the Qimme2 documentation.

Below we list the actions available in q2-mosphit. Each action has its dedicated wiki page where you will find input and output descriptions, example use, and citations. Some also contain links to relevant resources.

Analysis Actions

The following actions perform some kind of analysis on the input data.

Action	Description
bin-contigs-metabat	This method uses MetaBAT 2 to bin contigs into MAGs.
classify-kaiju	Classify reads using Kaiju.
classify-kraken2	Perform taxonomic classification of reads or MAGs using Kraken 2.
dereplicate‐mags	Dereplicate MAGs from multiple samples.
eggnog-annotate	Annotate hits using the eggNOG annotation database.
eggnog-diamond-search	Find homolog sequences in contigs or MAGs against a Diamond database.
eggnog-hmmer-search	Find homolog sequences in contigs or MAGs against a HMMER database. TODO
estimate-bracken	Perform read abundance re-estimation using Bracken.
evaluate‐busco	Use BUSCO to assess the quality of assembled MAGs.
kraken2-to-features	Select downstream features from Kraken 2.
kraken2-to-mag-features	Select downstream MAG features from Kraken 2.
predict-genes-prodigal	This action uses Prodigal for gene prediction.
inspect-kraken2-db	Inspect a Kraken 2 database.

Build or Fetch Database Actions

These actions fetch or build databases that will be used as input in other actions.

Action	Description
build-custom-diamond-db	Creates a Diamond database from a custom protein database.
build-eggnog-diamond-db	Creates a Diamond database for a specific taxon.
build-kraken-db	Build Kraken 2 database.
fetch‐busco‐db	Downloads BUSCO database for the specified lineage.
fetch-diamond-db	Downloads the full diamond reference database.
fetch-eggnog-db	Download the eggNOG annotation database.
fetch-eggnog-proteins	Downloads eggNOG protein database.
fetch-eggnog-hmmer-db	Downloads the profile HMMs and other files for a given taxon.
fetch-kaiju-db	Download Kaiju database.
fetch-ncbi-taxonomy	Downloads NCBI reference taxonomy.

Partition and Collate Actions

Partition

Partition-actions take artifacts that contain multiple files (e.g. different fasta files from different samples or different fasta files for the same sample) and create several artifacts with a subset of the initial files (e.g. one fasta file per artifact). This action is often useful when looking to run the same action in parallel with smaller chunks of the input.

Action	Description
partition-orthologs	Partition a SampleData[BLAST6] artifact.
partition‐sample‐data‐mags	Partition a SampleData[MAGs] artifact.
partition‐feature‐data‐mags	Partition a FeatureData[MAG] artifact.

Collate

The collate-actions do the exact opposite. They take a collection of artifacts of the same semantic type and aggregate them into one artifact. Usually one uses these actions after having partitioned and processed data to collect it again under the same file.

Action	Description
collate-orthologs	Collate SampleData[BLAST6]s.
collate-annotations	Collate FeatureData[NOG]s.
collate‐sample‐data‐mags	Collate SampleData[MAGs]s.
collate‐feature‐data‐mags	Collate FeatureData[MAG]s.

Relevant Actions Outside of q2-mosphit

The Qimme2 CLI offers some very useful tools for you to interact, create, and inspect artifacts. We list some that we think are particularly relevant.

Action	Description
qiime tools import	Import data into a Qimme2 artifact.
qiime tools extract	Extract data from a Qiim2 artifact.
qiime tools citations	List citations relevant to the creation of an artifact.