QIIME 2 plugin for (meta)genome assembly.
To install q2-assembly, follow the installation steps described below.
mamba create -yn q2-shotgun \
-c https://packages.qiime2.org/qiime2/2022.8/tested \
-c bioconda -c conda-forge -c default q2-assembly q2cli
conda activate q2-shotgunRefresh cache and check that everything worked:
qiime dev refresh-cache
qiime infoThis QIIME 2 plugin contains actions used to assemble (meta)genomes from short single/paired-end sequencing reads. Currently, two assemblers are supported: SPAdes and MEGAHIT (for details on the implementation and usage, please refer to the respective documentation). Below you will find an overview of actions available in the plugin.
| Action | Description | Underlying tool |
|---|---|---|
| assemble-megahit | Assemble contigs using MEGAHIT. | MEGAHIT |
| assemble-spades | Assemble contigs using SPAdes. | SPAdes |
| evaluate-contigs | Evaluate quality of the assembled contigs using metaQUAST. | QUAST |
| generate-reads | Simulate NGS reads using InSilicoSeq. | InSilicoSeq |
| index-contigs | Index contigs using Bowtie 2. | Bowtie 2 |
| index-mags | Index MAGs using Bowtie 2. | Bowtie 2 |
| map-reads-to-contigs | Map reads to contigs using Bowtie 2. | Bowtie 2 |
This repository follows the black code style. To make the development slightly easier
there are a couple of pre-commit hooks included here that will ensure that your changes
follow that formatting style. Before you start working on the code, please
install the hooks by executing make dev in your conda environment. From then on,
they will be run automatically every time you commit any changes.