MitoFinder version 1.4.2

Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link)

<p align="center"> <img src="/image/logo.png" alt="Drawing" width="250"/> </p>

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Requirements

This software is suitable for all linux-like systems with automake, autoconf, gcc (Unfortunately not Windows < v.10) or Singularity version >= 3.0 installed. The pipeline is mainly written in python 2.7.

Table of content

1. Installation guide for MitoFinder
   • RECOMMENDED - Using Singularity version >=3.0
   • Linux
   • MAC
2. How to use MitoFinder
   • Mitochondrial genome assembly and annotation
   • Find and/or annotate a mitochondrial genome
   • Restart
   • Test cases
3. Detailed options
4. INPUT FILES
5. OUTPUT FILES
6. Particular cases
7. UCE annotation
8. How to cite MitoFinder
9. How to get reference mitochondrial genomes from ncbi
10. How to submit your annotated mitochondrial genome(s) to GenBank NCBI

Installation guide for MitoFinder

Run MitoFinder with Singularity

There are many cases where using a singularity container would be easier than installing MitoFinder from source. In particular, if you are working on a server (without administrator rights) or if your default version of python is python 3.x, I recommend you to use the singularity container available here to run MitoFinder.

→ How to install Singularity version >= 3.0

Since you have Singularity version >= 3.0 installed, you can clone MitoFinder's container directly using singularity with the following command:

singularity pull --arch amd64 library://remiallio/default/mitofinder:v1.4.2 

and then run it as follows:

singularity run mitofinder_v1.4.2.sif -h  

or:

mitofinder_v1.4.2.sif -h  

Then, you can get MitoFinder test cases (optional)
→ See MitoFinder_container github page. To clone this reduced repository:

git clone https://github.com/RemiAllio/MitoFinder_container.git

Add MitoFinder's container to your path

cd PATH/TO/MITOFINDER_IMAGE/
p=$(pwd)
echo -e "\n#Path to MitoFinder image \nexport PATH=\$PATH:$p" >> ~/.bashrc 
source ~/.bashrc  

WARNING: If you previously installed MitoFinder on your system and want to install a new version, you should replace the old MitoFinder PATH by the updated one in your ~/.bashrc file. To do so, you need to edit your ~/.bashrc file, remove the lines that add MitoFinder to the PATH, and close your terminal. Then, you should open a new terminal and re-execute the command lines from above.
TIP: If you are connected to cluster, you can use either nano or vi to edit the ~/.bashrc file.

To check if the right version of MitoFinder is actually in your PATH:

mitofinder_v1.4.2.sif -v

Get and install MitoFinder (Linux)

/!* WARNING **/!*: MitoFinder is written in python2.7 (I recommend to use the singularity image if your python default version is python3.+. Otherwise, you may encounter some issues associated with python2.7 dependencies.

Before starting, MitoFinder installation requires automake and autoconf to be installed. Even if these two tools are often already installed in the linux system, here is the command to install them if necessary:

sudo apt-get install automake autoconf  

If you want to use MiTFi for the tRNA annotation step (recommended), java needs to be installed. Here is the command to install it:

sudo apt install default-jre

(optional) If you want to generate images (annotated contigs), you will need the package pillow:

pip2.7 install pillow==6.2.2

Clone MitoFinder from GitHub

git clone https://github.com/RemiAllio/MitoFinder.git
cd MitoFinder
./install.sh

PATH/TO/MITOFINDER/mitofinder -h  

or download master.zip

wget https://github.com/RemiAllio/MitoFinder/archive/master.zip
unzip master.zip
mv MitoFinder-master MitoFinder
cd MitoFinder
./install.sh

PATH/TO/MITOFINDER/mitofinder -h  

Add MitoFinder to your path

cd PATH/TO/MITOFINDER/
p=$(pwd)
echo -e "\n#Path to MitoFinder \nexport PATH=\$PATH:$p" >> ~/.bashrc 
source ~/.bashrc  

WARNING: If you previously installed MitoFinder on your system and want to install a new version, you should replace the old MitoFinder PATH by the updated one in your ~/.bashrc file. To do so, you need to edit your ~/.bashrc file, remove the lines that add MitoFinder to the PATH, and close your terminal. Then, you should open a new terminal and re-execute the command lines from above.
TIP: If you are connected to cluster, you can use either nano or vi to edit the ~/.bashrc file.

To check if the right version of MitoFinder is actually in your PATH:

mitofinder -v

Get MitoFinder and install dependencies (Mac OS)

To install MitoFinder in Mac OS, you need automake and autoconf to be installed. The easiest way to install it (if necessary) is to use Homebrew as follow:

brew install autoconf automake

Get MitoFinder

Clone MitoFinder from GitHub

git clone https://github.com/RemiAllio/MitoFinder.git
cd MitoFinder
./install.sh

or download master.zip

wget https://github.com/RemiAllio/MitoFinder/archive/master.zip
unzip master.zip
mv MitoFinder-master MitoFinder
cd MitoFinder
./install.sh

Install dependencies

Once installed, you need to indicate the paths to the directory containing the executables on the Mitofinder.config file.
TIPS:
(1) If the executable is in your PATH, to find it you can use which. For example, which megahit.
(2) If not, you can go to the directory containing the executable and use pwd to get the PATH. Then, you can copy the PATH in the Mitofinder.config file.

BLAST

Given that MitoFinder uses makeblastdb, blastn, and blastx, you need to download the associated binaries available here. TIP: wget can be install with Homebrew using brew install wget

wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-macosx.tar.gz  
tar -xvf ncbi-blast-*-x64-macosx.tar.gz 
cd ncbi-blast-*+/bin/

Once downloaded, you need to indicate the PATH to the directory containing the binaries makeblastdb, blastn, etc. in the Mitofinder.config file.

Assemblers

To get MitoFinder to work, you need to install at least one of the following assemblers.

• MEGAHIT

Installation with conda (miniconda2 or anaconda2):

conda install -c bioconda megahit

Once installed, you need to indicate the PATH to the directory containing the exectutable megahit in the Mitofinder.config file.
If you install megahit with conda, the executable will be in the miniconda/anaconda bin directory.
For example : /Users/remiallio/bin/miniconda2/bin/

• MetaSPAdes

We recommend to download the pre-compiled binaries:

curl http://cab.spbu.ru/files/release3.14.0/SPAdes-3.14.0-Darwin.tar.gz -o SPAdes-3.14.0-Darwin.tar.gz
tar -zxf SPAdes-3.14.0-Darwin.tar.gz
cd SPAdes-3.14.0-Darwin/bin/

Once downloaded, you need to indicate the PATH to the directory containing the exectutable metaspades.py in the Mitofinder.config file.

• IDBA-UD

To our knowledge, IDBA-UD is not supported for Mac OS at the moment.

tRNA annotation

• MiTFi and tRNAscan-SE should be installed by MitoFinder when running the install.sh.

However, MiTFi requires java to be installed. If java is not installed, you can download the .dmg file to install it [here](https://www.oracle.com/java/technologies/javase-