QIIME 2 plugin for (meta)genome assembly.
q2-assembly 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 assemble (meta)genomes from short single/paired-end sequencing reads:
| 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-derep-mags | Index dereplicated MAGs using Bowtie2. | Bowtie 2 |
| index-mags | Index MAGs using Bowtie 2. | Bowtie 2 |
| map-reads | Map reads to contigs/MAGs using Bowtie 2. | Bowtie 2 |
| rename-contigs | Rename contigs using unique IDs. | - |
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.