Kaiju script

[valeriafloral]

Hi,
I assume that your file with right mates and the file with left mates contains the same number of reads and the reads are in the same order in both files.

Then you can just run Kaiju twice and combine the output of both runs.

First, run Kaiju with the intact read pairs in paired-end mode:

kaiju -i leftmates.fastq -j rightmates.fastq -o pairedreads.out ...

Second, run the singletons:

kaiju -i singletons.fastq -o singletons.out ...

Then just concatenate them

cat pairedreads.out singletons.out > combined.out

Now you can run kaijuReport or kaiju2krona etc on the combined.out file.

Originally posted by @pmenzel in bioinformatics-centre/kaiju#9 (comment)