Use kraken2, KronaTools to analysis DNA NGS metagenomics

run.sh

cd ~
git clone https://github.com/DerrickWood/kraken2.git -b v2.1.2
cd kraken2/

./install_kraken2.sh bin

~/kraken2/bin/kraken2-build --download-taxonomy --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library human --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library archaea --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library bacteria --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library fungi --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library plant --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library plasmid --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library protozoa --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library viral --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library nr --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library nt --protein --db db_protein
~/kraken2/bin/kraken2-build --threads $(nproc) --build --protein --db db_protein
bin/kraken2-build --clean --db db_protein

~/kraken2/bin/kraken2-build --download-taxonomy --db db_nucleotide
#~/kraken2/bin/kraken2-build --download-library human --db db_nucleotide
~/kraken2/bin/kraken2-build --download-library archaea --db db_nucleotide
~/kraken2/bin/kraken2-build --download-library bacteria --db db_nucleotide
~/kraken2/bin/kraken2-build --download-library fungi --db db_nucleotide
#~/kraken2/bin/kraken2-build --download-library plant --db db_nucleotide
#~/kraken2/bin/kraken2-build --download-library plasmid --db db_nucleotide
~/kraken2/bin/kraken2-build --download-library protozoa --db db_nucleotide
~/kraken2/bin/kraken2-build --download-library viral --db db_nucleotide
#~/kraken2/bin/kraken2-build --download-library nt --db db_nucleotide
#~/kraken2/bin/kraken2-build --download-library UniVec --db db_nucleotide
~/kraken2/bin/kraken2-build --threads $(nproc) --build --db db_nucleotide
bin/kraken2-build --clean --db db_nucleotide

cd ..

#~/kraken2/bin/kraken2 --db ~/kraken2/db_protein \
~/kraken2/bin/kraken2 --db ~/kraken2/db_nucleotide \
 --threads $(nproc) \
 --memory-mapping \
 --output sampleName.microbe-classification.tsv \
 --report sampleName.microbe-classification-report.tsv \
 --paired sampleName_R1.fastq.gz sampleName_R2.fastq.gz

wget https://github.com/marbl/Krona/releases/download/v2.8.1/KronaTools-2.8.1.tar
tar axvf KronaTools-2.8.1.tar
cd KronaTools-2.8.1/
./install.pl --prefix .
./updateTaxonomy.sh
cd ..

~/KronaTools-2.8.1/bin/ktImportTaxonomy -q 2 -t 3 sampleName.microbe-classification.tsv -o sampleName.krona.chart.html