generated from bokulich-lab/q2-plugin-template
-
Notifications
You must be signed in to change notification settings - Fork 14
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
51 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,46 @@ | ||
| # q2-moshpit | ||
|  | ||
|  | ||
| [](https://codecov.io/gh/bokulich-lab/q2-moshpit) | ||
|
|
||
| **MO**dular **SH**otgun metagenome **P**ipelines with **I**ntegrated provenance **T**racking | ||
| QIIME 2 plugin for functional annotation and taxonomic classification of shotgun metagenomes. | ||
|
|
||
| ## Installation | ||
| _q2-moshpit_ is available as part of the QIIME 2 metagenome distribution. For installation and usage instructions please consult the official [QIIME 2 documentation](https://www.docs.qiime2.org). | ||
|
|
||
| ## Functionality | ||
| This QIIME 2 plugin contains actions used to annotate and classify (meta)genomes. | ||
| Below you will find an overview of actions available in the plugin. | ||
|
|
||
| | 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. | - | | ||
| | eggnog-annotate | Annotate orthologs against eggNOG database. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) | | ||
| | eggnog-diamond-search | Run eggNOG search using diamond aligner. | [EggNOG mapper](https://github.com/eggnogdb/eggnog-mapper) | | ||
| | eggnog-hmmer-search | 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) | |
10 changes: 10 additions & 0 deletions
10
environment-files/q2-moshpit-qiime2-metagenome-2024.10.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| channels: | ||
| - https://packages.qiime2.org/qiime2/2024.10/metagenome/passed | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - qiime2-metagenome | ||
| - pip | ||
| - pip: | ||
| - q2-moshpit@git+https://github.com/bokulich-lab/q2-moshpit.git@main | ||
|
|