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MitoZ 3.0

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@linzhi2013 linzhi2013 released this 01 May 21:01
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3.0
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Learn about vigilant mode.

MitoZ 3.0 is coming.

Now MitoZ uses the Fastp program for raw data filtering, which is faster. Users are also allowed to specify multiple kmers directly for assembly via mitoz all or mitoz assemble commands (which could help some samples), you can also define your own profile directory path.

Now you can install MitoZ via

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba create -n mitozEnv -c bioconda mitoz=3.0
$ source activate mitozEnv   # or use "mamba" or "conda" instead of "source" the command here.

$ circos --modules # check if all Perl modules required by circos are installed. Some modules could still be missing (don't know why conda did not fix them automatically). Similar problems can be seen at https://github.com/bioconda/bioconda-recipes/issues/9830

# For me, the Perl modules "GD" and "GD::Polyline" were missing (although conda said they have been installed already when I ran 'conda install perl-gd'), I fixed them by running following three commands:
$ mamba install -c conda-forge pkg-config
$ mamba install -c anaconda gcc_linux-64
$ cpanm install GD
# I will try to fix the circos' problem in bioconda's MitoZ recipe file, but for the moment, please use the above solution, or try the "mitozEnv.yaml" solution below.
# You can use the ”cpanm“ command to install other missing Perl modules if necessary. 

# Now we are ready to go:
$ mitoz # all subcommands are within this command now!

$ mitoz-tools # some useful tools for mitochondrial genome analysis

I do not have enough time to update the documentation yet, but you can start to play with the mtioz and mitoz-tools commands now.

More features are coming.

If the above installation method does not work for you, you can try

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba env create -n mitozEnv  -f mitozEnv.yaml
$ conda activate mitozEnv
$ pip install ./mitoz-3.0.tar.gz
# or 
$ tar -zxvf mitoz-3.0.tar.gz
$ cd mitoz-3.0
$ python3 setup.py install

For the moment, MitoZ runs on Linux only. Mac OS platform is not fully supported yet, maybe later we can fix this.

If there are bugs, you can try the older version 2.3, and raise issues to report bugs, thanks!

image

Citations
Specifically, when you use MitoZ for data analysis, you should cite both the MitoZ paper and the related software invoked by MitoZ.

  • fastp # for the all or filter subcommand (MitoZ version >= 3.0)
  • soapdenovo-trans # for the all or assemble subcommand
  • hmmer # for the all or assemble or findmitoscaf subcommand
  • blast # for the all or assemble or findmitoscaf or annotate subcommand
  • genewise # for the all or assemble or findmitoscaf or annotate subcommand
  • infernal # for the all or annotate subcommand
  • MiTFi # for the all or annotate subcommand
  • cricos # for the all or annotate or visualize subcommand
  • bwa # for the all or annotate or visualize subcommand and you draw the sequencing coverage distribution track
  • samtools # for the annotate or visualize subcommand and you draw the sequencing coverage distribution track

Please refer to the MitoZ paper for the reference details.

From now on, I will use Wiki (https://github.com/linzhi2013/MitoZ/wiki) to give more explanation on how to use MitoZ.

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