MitoZ 3

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About:

• MitoZ provides a "one-click" solution to get annotated mitogenomes from raw data fastq files.

News

• (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)!

• For Windows Sublinux users, you might need to recompile the cmsearch program for tRNA annotation.

• (April-20-2023) Docker and Singularity versions of MitoZ 3.6 come out now. Both were tested on Ubuntu 20.04.4 LTS.

• (April-19-2023) On the installation problem (#188), hopefully now it is fixed. Please let me know if it is not.

• (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 (firstly recommended if the conda way does not work for you), conda and source code.

See

• Installation: https://github.com/linzhi2013/MitoZ/wiki/Installation.
• MAKE SURE that you do a test run using provided test dataset before running your own samples!.
• Tutorial: https://github.com/linzhi2013/MitoZ/wiki/Tutorial (Recommended if you are NEW to MitoZ!)
• Documentation: https://github.com/linzhi2013/MitoZ/wiki and the HMTL version. The HTML version may not be update-to-date.
• Latest release: https://github.com/linzhi2013/MitoZ/releases/

Bugs and Questions

• Have a look at https://github.com/linzhi2013/MitoZ/issues and https://github.com/linzhi2013/MitoZ/wiki/Known-issues for known bugs or issues.

• Please try the latest version first if you find some bugs in the old versions

  • to do that, you should specify the version of MitoZ when you use the mamba/conda command (please refer to the installation instruction), as I found out that many people still download the older versions.

• 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 #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 #187 for the current solution.

• check which shell you are using:

  $ echo "$SHELL"
  

• 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.

• 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!

• Any feedbacks are wellcome!

Citations

• 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
• Additionally, please cite the related software invoked by MitoZ: https://github.com/linzhi2013/MitoZ/wiki/Citations