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Welcome to the MitoZ wiki!

$ mitoz -h
usage: mitoz [-h] [--version] [--debug] {filter,assemble,findmitoscaf,annotate,visualize,all} ...

MitoZ 3.6

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
PERFORMANCE OF THIS SOFTWARE.

WHEN YOU ADAPT (PART OF) THE SOFTWARE FOR YOUR USE CASES, THE AUTHOR AND
THE SOFTWARE MUST BE EXPLICITLY CREDITED IN YOUR PUBLICATIONS AND SOFTWARE,
AND YOU SHOULD ASK THE USERS OF YOUR SOFTWARE TO CITE THE SOFTWARE IN
THEIR PUBLICATIONS. IN A WORD, 请讲武德.

COPYRIGHT 2019-2022 Guanliang Meng. ALL RIGHTS RESERVED.

When you use MitoZ, please cite:
Meng, G., Li, Y., Yang, C., & Liu, S. (2019). MitoZ: a toolkit for
animal mitochondrial genome assembly, annotation and visualization.
Nucleic acids research, 47(11), e63-e63. https://doi.org/10.1093/nar/gkz173

Additionaly, you SHOULD also CITE related software invoked by MitoZ,
without them, MitoZ will not make its way. For more details, please
refer to the MitoZ paper and https://github.com/linzhi2013/MitoZ.

positional arguments:
  {filter,assemble,findmitoscaf,annotate,visualize,all}
    filter              Filter input fastq reads.
    assemble            Mitochondrial genome assembly from input fastq files.
    findmitoscaf        Search for mitochondrial sequences from input fasta file.
    annotate            Annotate PCGs, tRNA and rRNA genes.
    visualize           Visualize input GenBank file.
    all                 Run all steps for mitochondrial genome anlysis from input fastq files.

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --debug               debug mode output [False]