MITOPORE command line tool manual

Getting start

We recommend to use our Docker at thachdt4. If you use Docker you can skip this installation part and read the "Run mitopore_workflow pipeline" part below.

Installation locally

Mitopore_workflow local version requires python3 and works on Unix liked environment. Simply install Python3 and run the code below(you may have to run it as a sudo user on Linux):

git clone [email protected]:thachnguyen/mitopore_workflow.git
cd mitopore_workflow/mitopore_local
python install.py

Install R and Bioconductor packages

Install R version 4.x https://docs.posit.co/resources/install-r-source/#specify-r-version
R packages:

• tidyverse
• yaml
• gridExtra
• stringr
• vcfR

R Bioconductor:

• EnsDb.Hsapiens.v86
• ShortRead

Run mitopore_workflow pipeline

Data Preparation

Mitopore workflow supports multiple fastq files. The user must store all the fastq files in a single fastq folder.
testdata_directory/fastq/sample1.fastq
testdata_directory/fastq/sample2.fastq
testdata_directory/fastq/sample3.fastq

Mitopore_workflow has two pipelines, user can run one of two command below. Depend on Python interpreter you may have to use python3 instead of python. We have a small test data on this repository.

Using Docker container

SNV calling

docker run -v /test_data_absolute_path/on/your_machine:/mitopore_data/ -i thachdt4/mitopore_local:latest python /home/ag-rossi/projects/mitopore_workflow/mitopore_local/mitopore_snv.py

you have to change the /test_data_absolute_path/on/your_machine to the path where you store the data

INDEL calling (Beta version)

docker run -v /test_data_absolute_path/on/your_machine:/mitopore_data/ -i thachdt4/mitopore_local:latest python /home/ag-rossi/projects/mitopore_workflow/mitopore_local/mitopore_indel.py 

INDEL calling (ILLUMINA DATA)

When you use Illumina data, preprocessing is not required so please use this command with Illumina flag

docker run -v /test_data_absolute_path/on/your_machine:/mitopore_data/ -i thachdt4/mitopore_local:latest python /home/ag-rossi/projects/mitopore_workflow/mitopore_local/mitopore_indel.py /mitopore_data/ illumina

you have to change the /test_data_absolute_path/on/your_machine to the path where you store the data 
##### Optional parameters
Running parameters are preset in config.yaml. 

#### Installation on local machine (for experienced user)
##### SNV calling
```console
python mitopore_snv.py testdata_directory_path 

E.g. use "python mitopore_snv.py ../testdata" for our test data

INDEL calling (Beta version)

python mitopore_indel.py testdata_directory_path 

E.g. use "python mitopore_indel.py ../testdata" for our test data

INDEL calling (ILLUMINA DATA)

When you use Illumina data, preprocessing is not required so please use this command with Illumina flag

python mitopore_snv.py testdata_directory_path illumina

mitopore_indel.py illumina E.g. use "python mitopore_indel.py ../testdata illumina" for our test data

Optional parameters

Running parameters are preset in config.yaml.

Results

The result is summarized in a single HTML file report.html in your testdata_directory. Other supplementary result files (graphical plots, BAM alignment files, coverage, and mapping reports ...)are in the Results folder and Analysis folder.

System requirement

* CPU: 2.0 GHz (64bits) 2 cores or higher
* Memory: 24 GB or higher
* Diskdrive: 100 GB free space 
* Linux (64 bits) or MacOS.

Dependencies

All dependent packages are described in install.py files