Running Kraken2 and creating a Krona report

 Had to work with Ion Torrent BAMs for this but I think it's applicable to everything

  Needed to run this on unmapped reads so running this first.

	#!/bin/bash
	samtools view -b -f 4 $1 > $1.unmapped.bam
	samtools index $1.unmapped.bam
	java -Xmx8g -jar /opt/picard/picard-tools-current/picard.jar SamToFastq I=$1.unmapped.bam F=$1.unmapped.bam.fastq
	/home/ionadmin/bin/bbmap/reformat.sh in=$1.unmapped.bam.fastq out=$1.unmapped.bam.fastq.fasta
	gzip $1.unmapped.bam.fastq.fasta

view raw extract-unmapped-reads-bam.sh hosted with ❤ by GitHub

After that the next script is fairly simple 

	~/bin/kraken2/kraken2 --db ~/k2_standard_16gb_20210517 --use-names --gzip-compressed $1 --output $1.kraken --report $1.kraken.report
	cut -f2,3 $1.kraken > $1.kraken.kronainput
	ktImportTaxonomy -tax /home/kev/Krona-master/KronaTools/taxonomy $1.kraken.kronainput -o $1.kraken.kronainput.html

view raw run-kraken-krona.sh hosted with ❤ by GitHub

Will share the install when I have time. A major hiccup for me was realising not all pre-built db works with Kraken2