This pipeline filter your input sequences based on Kaiju (Menzel, P. et al. (2016), Github page) output. It was developed as part of the CRC1182 and inspired by the workflow used by Schmittmann et al 2021.
When working with metaorganisms, is often desired to filter out sequencing reads from one symbiosis entities. This is what this pipeline is designed for. For instance, Schmittmann et al 2021 used this approach to filter out putative microbial reads from the transcriptome of sponge Halichondria panicea before de novo assembly of the transcriptome.
This pipeline does not contain novel algorithms. These are based on the following softwares: