Metadata-Version: 2.4
Name: q2-assembly
Version: 2026.7.0.dev0
Summary: QIIME 2 plugin for (meta)genome assembly.
Author-email: Michal Ziemski <ziemski.michal@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2025, QIIME 2 development team.
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of the copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Homepage, https://github.com/bokulich-lab/q2-assembly
Project-URL: Repository, https://github.com/bokulich-lab/q2-assembly
Description-Content-Type: text/markdown
License-File: LICENSE
Dynamic: license-file

# q2-assembly
![CI](https://github.com/bokulich-lab/q2-assembly/actions/workflows/ci.yaml/badge.svg)
[![codecov](https://codecov.io/gh/bokulich-lab/q2-assembly/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-assembly)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

QIIME 2 plugin for (meta)genome assembly.

## Installation
_q2-assembly_ is available as part of the QIIME 2 moshpit distribution. For installation and usage instructions please consult the official [QIIME 2 documentation](https://docs.qiime2.org).

## Functionality
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](https://github.com/voutcn/megahit)           |
| assemble-spades        | Assemble contigs using SPAdes.                             | [SPAdes](https://github.com/ablab/spades)              |
| evaluate-quast         | Evaluate quality of the assembled contigs using metaQUAST. | [QUAST](https://github.com/ablab/quast)                |
| filter-contigs         | Filter contigs by length and/or metadata.                  | -                                                      |  
| generate-reads         | Simulate NGS reads using InSilicoSeq.                      | [InSilicoSeq](https://github.com/HadrienG/InSilicoSeq) |
| index-contigs          | Index contigs using Bowtie 2.                              | [Bowtie 2](https://github.com/BenLangmead/bowtie2)     |
| index-derep-mags       | Index dereplicated MAGs using Bowtie2.                     | [Bowtie 2](https://github.com/BenLangmead/bowtie2)     |
| index-mags             | Index MAGs using Bowtie 2.                                 | [Bowtie 2](https://github.com/BenLangmead/bowtie2)     |
| map-reads              | Map reads to contigs/MAGs using Bowtie 2.                  | [Bowtie 2](https://github.com/BenLangmead/bowtie2)     |
| rename-contigs         | Rename contigs using unique IDs.                           | -                                                      |
| simulate-reads-mason   | Simulate short reads using Mason.                          | [Mason](https://www.seqan.de/apps/mason.html)          |

## 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.
