# KRAKEN TOOLS

## Step 1: Clone repo "KrakenTools"

git clone https://github.com/jenniferlu717/KrakenTools.git

## Step 2: Make sure bio installed

pip3 install bio

## Step 3a: Run extract reads exclude Human TaxID from fastq - output : fastq

python3 KrakenTools/extract_kraken_reads.py -k <sample_name>.kraken --taxid 9606 --exclude -s <sample_name>_R1.fastq.gz -s2 <sample_name>_R2.fastq.gz -o <sample_name>_R1_extracted.fastq -o2 <sample_name>_R2_extracted.fastq --fastq-output

## Step 3b: Run extract reads exclude Human TaxID from fastq - output : fastq.gz

python3 KrakenTools/extract_kraken_reads.py -k <sample_name>.kraken --taxid 9606 --exclude -s <sample_name>_R1.fastq.gz -s2 <sample_name>_R2.fastq.gz -o <sample_name>_R1_extracted.fastq.gz -o2 <sample_name>_R2_extracted.fastq.gz --fastq-output