diff --git a/README.md b/README.md index 890d9ffe..447e986a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,46 @@ # q2-moshpit ![CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/ci.yaml/badge.svg) -![QIIME CI](https://github.com/bokulich-lab/q2-moshpit/actions/workflows/q2-ci.yaml/badge.svg) [![codecov](https://codecov.io/gh/bokulich-lab/q2-moshpit/graph/badge.svg?token=PSCAYJUP01)](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) | diff --git a/environment-files/q2-moshpit-qiime2-metagenome-2024.10.yml b/environment-files/q2-moshpit-qiime2-metagenome-2024.10.yml new file mode 100644 index 00000000..156815b3 --- /dev/null +++ b/environment-files/q2-moshpit-qiime2-metagenome-2024.10.yml @@ -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 + \ No newline at end of file