MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking
QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes.
q2-moshpit is available as part of the QIIME 2 metagenome distribution. For installation and usage instructions please consult the official QIIME 2 documentation.
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. | - |
| eggnog-annotate | Annotate orthologs against eggNOG database. | EggNOG mapper |
| eggnog-diamond-search | Run eggNOG search using diamond aligner. | EggNOG mapper |
| eggnog-hmmer-search | 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 |