MetONTIIME

[amatoute]

Dear,

I am working on an 18S sequencing project. For that I have to analyze my data and I have no programming skills. I am interested in the MetONTIIME workflow, do you have a demonstration of the installation in video or a tutorial with more details?

Best regards

[MaestSi]

Hi, unfortunately no, all instructions I have are collected in the README. If you want to try it yourself, I am happy to help. Otherwise, I’m also open to collaborations; in case you are interested in that, just reach out to me by e-mail! Best, Simone

[amatoute]

Hi,

Yes, I need some help to execute this program.

Yes we can collaborate but I would like to learn during this collaboration and improve my skills in bioinformatics. To introduce myself, my name is Adria MATOUTE and I'm working for a biology lab in the University of French Guiana (in south america).

To execute this program, the first step was to install miniconda3. Than I installed MetONTIIME using this script :

PIPELINE_DIR=$(realpath $( dirname "${BASH_SOURCE[0]}" ))

MINICONDA_DIR=$(which conda | sed 's/miniconda3.*$/miniconda3/')

conda config --add channels bioconda

conda config --add channels conda-forge

conda config --add channels r

conda config --add channels anaconda

wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml

conda env create -n MetONTIIME_env --file qiime2-2022.2-py38-linux-conda.yml

rm qiime2-2022.2-py38-linux-conda.yml

source activate MetONTIIME_env => entréey

conda install seqtk NanoFilt

pip install pycoQC

echo -e "\n"

echo "Modify variables PIPELINE_DIR and MINICONDA_DIR in config_MinION_mobile_lab.R"

echo -e "PIPELINE_DIR <- \"$PIPELINE_DIR\""

echo -e "MINICONDA_DIR <- \"$MINICONDA_DIR\""

echo -e "\n"

I'm not sure that the echo tool make the good path for the variable and I can't find out where the script " [ https://github.com/MaestSi/MetONTIIME/blob/master/config_MinION_mobile_lab.R | config_MinION_mobile_lab.R ] " is physically located on the compunter.

Best regard,

Adria MATOUTE

UMR-CIIL - Laboratoire TBIP

Université de Guyane

+33 6 31 24 73 37

[MaestSi]

Ciao Adria, Nice to meet you. Could you just run the install.sh script as described in the readme (and not just the content of the file) and please tell me which are the suggested paths for the pipeline and miniconda dirs? The config script is inside the pipeline dir that you downloaded where you performed the git clone command. Best, Simone

[amatoute]

Dear,

When I executing the command with install.sh I was able to modify the script config_MinION_mobile_lab.R with a text editor. What is the next stage after ? I have to follow the section Starting analysis from fastq.gz files after ? An other question, during the expirementation, I use an other barcode kit and other flowcell, can I change that in the script config_MinION_mobile_lab.R ?

Adria

[MaestSi]

The next stage depends on whether you have already base-called and demultiplexed your data or you have raw fast5 files. Yes, you can change the kit and flow-cell in the config file, but this will have an effect only if you start the analysis from raw fast5 files. Best, Simone

[amatoute]

I already basecalled and demultiplexing my data with nanopore software. Now, I have raw data in fastq files.

Adria

[MaestSi]

Ok, so you don’t need to modify the config file, just gzip your files and follow the instructions in the readme at the “Starting the analysis from fastq.gz files” section. Best, Simone

[amatoute]

Ok, thank you, can you explain me the difference between and please ?

How I can use silvadatase wherease NCBI please, I'm working on 18S and not 16S?

Adria

[amatoute]

Also, can you give me a scale for all of the differents parameters please :

: maximum number of threads used : either Blast or Vsearch : maximum number of hits; if a value > 1 is used, a consensus taxonomy for the top hits is retrieved : minimum portion of a query sequence that should be aligned to a sequence in the database [0-1] : minimum alignment identity threshold [0-1] For exemple, if I put 5 for what's the meaning ? Adria

[MaestSi]

Please find all the information in QIIME2 documentations, which is the framework MetONTIIME is based on: https://docs.qiime2.org/2022.2/ If you have any other doubts which you can’t find in the docs, I’m happy to help. Best, Simone

[amatoute]

Can you suggest me a page of QIIME more focus on my issue please?

Adria

[MaestSi]

I’m out of office at the moment, and I don’t have a laptop with me. But you should check the page where taxonomic classifiers are introduced (check for something like classify-vsearch) and the introduction page with all the terms. Moreover, I suggest to read through the moving pictures tutorial. Simone

[MaestSi]

We'll continue the discussion offline, if you want. Just send me a private message to my e-mail address.