007

Extracting rRNA encoding reads and annotating them

sortmerna -n 2 --db \
/proj/g2014113/src/sortmerna-1.9/rRNA_databases/silva-arc-16s-database-id95.fasta \
/proj/g2014113/src/sortmerna-1.9/rRNA_databases/silva-bac-16s-database-id85.fasta \
--I /proj/g2014113/metagenomics/cta/reads/${s}_pe.fasta \
--accept ${s}_rrna \
--other ${s}_nonrrna  \
--bydbs  \
-a 8  \
--log ${s}_bilan  \
-m 5242880

java -Xmx1g -jar /glob/inod/src/rdp_classifier_2.6/dist/classifier.jar \
    classify \
    -g 16srrna  \
    -b `basename ${s}`.bootstrap  \
    -h `basename ${s}`.hier.tsv  \
    -o `basename ${s}`.class.tsv  \
    ${s}

Visualising taxonomy with KRONA