Kodoja

RNA-sequencing enables the detection of multiple plant viruses without prior hypotheses, but existing workflows are often tailored for human data. The new workflow, Kodoja, enhances plant virus detection by using k-mer profiling and sequence mapping, integrating Kraken and Kaiju tools. Tested on grapevine and raspberry RNA-seq datasets, Kodoja proved more sensitive than traditional methods, detecting more viruses and identifying lower virus amounts than RT-PCR. It also facilitated the design of new PCR primers for specific viruses. Kodoja is accessible via Bioconda and Galaxy, offering a sensitive approach for plant virus discovery.
Baizan-Edge et al. 2019 J Gen Virol 100(3): 533-42
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