├── .github └── ISSUE_TEMPLATE │ └── custom.md ├── LICENSE ├── README.md └── test ├── README.md ├── docker.all2.sh ├── test.R1.fq.gz ├── test.R2.fq.gz ├── test.result.tar.gz └── udocker_all2.sh /.github/ISSUE_TEMPLATE/custom.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/.github/ISSUE_TEMPLATE/custom.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # MitoZ 3 2 | GitHub release (latest SemVer) GitHub all releases GitHub 3 | [![docker build](https://img.shields.io/badge/docker%20build-passing-brightgreen)](https://hub.docker.com/r/guanliangmeng/mitoz/tags) [![docker latest version](https://img.shields.io/docker/v/guanliangmeng/mitoz)](https://hub.docker.com/r/guanliangmeng/mitoz/tags) [![docker pulls](https://img.shields.io/docker/pulls/guanliangmeng/mitoz?style=flat)](https://hub.docker.com/r/guanliangmeng/mitoz/tags) 4 | [![singularity image](https://img.shields.io/badge/Singularity%20build-passing-brightgreen)](https://github.com/linzhi2013/MitoZ/wiki/Installation#3-apptainersingularity) 5 | [![Conda-pack](https://img.shields.io/badge/conda--pack-passing-brightgreen)](https://github.com/linzhi2013/MitoZ/wiki/Installation#4-conda-pack) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://github.com/linzhi2013/MitoZ/wiki/Installation#5-conda) [ ](https://anaconda.org/bioconda/mitoz/badges/version.svg) [![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/mitoz)](https://anaconda.org/bioconda/mitoz) 6 | 7 | 8 | THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH 9 | REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY 10 | AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, 11 | INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM 12 | LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE 13 | OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR 14 | PERFORMANCE OF THIS SOFTWARE. 15 | 16 | **WHEN YOU ADAPT (PART OF) THE SOFTWARE FOR YOUR USE CASES, THE AUTHOR AND 17 | THE SOFTWARE MUST BE EXPLICITLY CREDITED IN YOUR PUBLICATIONS AND SOFTWARE, 18 | AND YOU SHOULD ASK THE USERS OF YOUR SOFTWARE TO CITE THE SOFTWARE IN 19 | THEIR PUBLICATIONS. IN A WORD, 请讲武德.** 20 | 21 | **About:** 22 | - **MitoZ provides a "one-click" solution to get annotated mitogenomes from raw data fastq files.** 23 | 24 | **News** 25 | - **(Nov 6, 2024)**: I found that using **too much raw data** (e.g. 12 Gbp) can lead to an un-circular mitogenome while using less raw data (e.g., 0.3 Gbp) can obtain a circular mitogenome (`mitoz all --assembler megahit --kmers_megahit 43 71 99`). So please try a smaller dataset (say, first 0.3 Gbp then 1 Gbp if fails) first and it is also less computationally intensive and much faster (when raw data is 0.3 Gbp, it used 8 CPUs, max RAM: 2GB, total run time: 10 mins)! 26 | 27 | - For Windows Sublinux users, you might need to recompile the `cmsearch` program for [tRNA annotation](https://github.com/linzhi2013/MitoZ/issues/208). 28 | 29 | - **(April-20-2023) [Docker](https://github.com/linzhi2013/MitoZ/wiki/Installation#1-docker) and [Singularity](https://github.com/linzhi2013/MitoZ/wiki/Installation#3-apptainersingularity) versions of MitoZ 3.6 come out now. Both were tested on Ubuntu 20.04.4 LTS.** 30 | 31 | - **(April-19-2023) On the installation problem (https://github.com/linzhi2013/MitoZ/issues/188), hopefully now it is fixed. Please let me know if it is not.** 32 | 33 | - **(April-14-2023) MitoZ 3.6 is just released (https://github.com/linzhi2013/MitoZ/releases/tag/3.6), fixed some bugs in MitoZ 3.5. It is recommended to upgrade to this version!** You can install it via **[conda-pack](https://github.com/linzhi2013/MitoZ/wiki/Installation#4-conda-pack)** (firstly recommended if the conda way does not work for you), [conda](https://github.com/linzhi2013/MitoZ/wiki/Installation#5-conda) and [source code](https://github.com/linzhi2013/MitoZ/wiki/Installation#6-source-codes). 34 | 35 | **See** 36 | - **Installation: https://github.com/linzhi2013/MitoZ/wiki/Installation**. 37 | - **MAKE SURE that you do a [test run](https://github.com/linzhi2013/MitoZ/wiki/Installation#9-running-the-test-dataset) using provided test dataset before running your own samples!**. 38 | - **Tutorial: https://github.com/linzhi2013/MitoZ/wiki/Tutorial (Recommended if you are NEW to MitoZ!)** 39 | - **Documentation: https://github.com/linzhi2013/MitoZ/wiki** and the [HMTL version](https://github.com/linzhi2013/MitoZ/releases/download/3.6/MitoZ_manual_v3.6.html). The HTML version may not be update-to-date. 40 | - **Latest release: https://github.com/linzhi2013/MitoZ/releases/** 41 | 42 | 43 | **Bugs and Questions** 44 | - Have a look at https://github.com/linzhi2013/MitoZ/issues and https://github.com/linzhi2013/MitoZ/wiki/Known-issues for known bugs or issues. 45 | 46 | - **Please try the latest version first if you find some bugs in the old versions** 47 | - to do that, you should specify the version of MitoZ when you use the `mamba/conda` command (please refer to the [installation instruction](https://github.com/linzhi2013/MitoZ/wiki/Installation)), as I found out that many people still download the older versions. 48 | 49 | - **Known bugs for MitoZ 3.5 (April-13-2023): (1) If your default shell is not bash, you can run into the missing annotation of tRNA genes (see https://github.com/linzhi2013/MitoZ/issues/187). Please change the default shell to bash before using MitoZ 3.5! (2) In MitoZ 3.5, I mistakenly used a `cmsearch` binary for Mac OS for Linux platform, which leads to the problem of failing to annotate any tRNA genes. Please check https://github.com/linzhi2013/MitoZ/issues/187 for the current solution.** 50 | 51 | - check which shell you are using: 52 | ``` 53 | $ echo "$SHELL" 54 | ``` 55 | 56 | 57 | - _I have been updating the documentation (wiki) from time to time, so it may be good for you to check the documentation again every after some time._ 58 | 59 | - In case there are still bugs in the latest version, please **firstly search https://github.com/linzhi2013/MitoZ/issues** and the Wiki to check whether similar questions have been raised by other users. If no related issues and answers are found, then please raise a new issue. Thank you! 60 | 61 | - Any feedbacks are wellcome! 62 | 63 | 64 | # Citations 65 | - Meng G, Li Y, Yang C, Liu S. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic acids research. 2019 Jun 20;47(11):e63-. https://doi.org/10.1093/nar/gkz173 66 | - Additionally, please cite the related software invoked by MitoZ: https://github.com/linzhi2013/MitoZ/wiki/Citations 67 | -------------------------------------------------------------------------------- /test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/test/README.md -------------------------------------------------------------------------------- /test/docker.all2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/test/docker.all2.sh -------------------------------------------------------------------------------- /test/test.R1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/test/test.R1.fq.gz -------------------------------------------------------------------------------- /test/test.R2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/test/test.R2.fq.gz -------------------------------------------------------------------------------- /test/test.result.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/test/test.result.tar.gz -------------------------------------------------------------------------------- /test/udocker_all2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linzhi2013/MitoZ/HEAD/test/udocker_all2.sh --------------------------------------------------------------------------------