metaKrak

This repository will help you master metagenomics with Kraken2.

official training site link ☁️

• Trimmomatic Usage
• Kraken2 Database

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Metagenomic with Kraken

III. install your working environment

• Start with conda conda installation

1. download the working directory ⬇️

wget https://github.com/Bboy010/metaKrak/archive/refs/heads/main.zip

2. unzip the folder 📥

sudo apt install unzip

unzip main.zip
rm –r  main.zip

3. create Conda environment 🐍

cd metaKrak

cd config-file/

conda env create -f metakrak.yml

conda activate metakrak
conda init

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4. Download Kraken2 🌍

Download directly and store in the metaKrak folder: metagenomic Note : The Kraken database zip is about 5 gb and the unzip 8 gb

wget https://genome-idx.s3.amazonaws.com/kraken/minikraken2_v2_8GB_201904.tgz

• Unzip the file

tar xfvz minikraken2_v2_8GB_201904.tgz

5. delete the zipped file 👽

rm minikraken2_v2_8GB_201904.tgz

6. Check the reposotory and create the folder data ✔️

ls
mkdir data
ls data

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7. Download Trimmomatic Data (Adapters) 🪚

wget https://raw.githubusercontent.com/usadellab/Trimmomatic/refs/heads/main/adapters/TruSeq3-PE.fa

8. Download fastq files (lib3-1 and 2) directly from Google Drive ⬇️

• file-1

lib3.R1_001.fastq.gz about 27 Mo

• file-2

lib3.R2_001.fastq.gz about 28 Mo

9. Store downloaded files in Data Folder 🏬

mv *.fastq.gz data/
ls/data

• at this stage you must have in your current folder

TruSeq3-PE.fa data minikraken2_v2_8GB_201904_UPDATE

ls # TruSeq3-PE.fa  data  minikraken2_v2_8GB_201904_UPDATE

10. Create Shortcuts 🚟

read1=data/lib3.R1_001.fastq.gz
read2=data/lib3.R2_001.fastq.gz

11. Run Trimmomatic 🪚

trimmomatic PE $read1 $read2 lib3.trimmed.paired.R1.fastq.gz lib3.trimmed.unpaired.R1.fastq.gz lib3.trimmed.paired.R2.fastq.gz lib3.trimmed.unpaired.R2.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:36

• Create folder to move trimmed data

mkdir trimmed
mv *.gz trimmed/

12. Create Shortcuts for Trimmed Data 🚟

read1=trimmed/lib3.trimmed.paired.R1.fastq.gz
read2=trimmed/lib3.trimmed.paired.R2.fastq.gz
krakendb=minikraken2_v2_8GB_201904_UPDATE

13. Run Kraken2 ✔️

mkdir kraken_report
kraken2 --use-names \
--db $krakendb \
--threads 2 \
--report kraken_report/lib3.report \
--paired --gzip-compressed $read1 $read2 > kraken_report/lib3.kraken

• checked output classified and unclassified

head kraken_report/lib3.report
head kraken_report/lib3.kraken

14. Visualization with Krona 👁️

• installation de krona

cd ~
git clone https://github.com/marbl/Krona.git
cd Krona/KronaTools
sudo ./install.pl

• Add Krona to PATH

export PATH=$PATH:~/Krona/KronaTools/bin
source ~/.bashrc

• Activate the environment again

conda activate metakrak

• Navigate to the report folder and extract necessary columns
• Extract data

tail -n +2 lib3.report | cut -f2,3,6 > lib3_krona_input.txt

15. Generate the HTML file with Krona 🧮

ktImportText lib3_krona_input.txt -o lib3_krona.html
explorer.exe lib3_krona.html

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