nbokulich / q2-assembly

QIIME 2 plugin for (meta)genome assembly.

q2-assembly

QIIME 2 plugin for (meta)genome assembly.

Installation

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-shotgun

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info

Functionality

This 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

Dev environment

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.