diff --git a/README.md b/README.md index d4c3c19c4d992ba496a9746ebd878543370dfb76..0ab04a34c6beaf845f4d5731e42e82e52333a3e3 100644 --- a/README.md +++ b/README.md @@ -84,13 +84,6 @@ conda deactivate ``` ## Viral metagenomic analysis - -Raw data were decontaminated by removing reads originating from carrots, cabbage, and turnip, as well as low-quality reads, in order to assemble the reads into contigs. Contigs longer than 2 kb were selected, and viral contigs were identified. - -All contigs larger than 2 kb were concatenated and dereplicated to retain only one vOTU. The cleaned reads were then mapped to the vOTUs to generate an abundance table of vOTUs in the samples. - -The abundance table was processed using the Virome_analyses_2024.rmd script in RStudio to create phyloseq objects for DNA- and RNA-amplified samples. - ### Reads QC For each sample, raw reads were quality quality checked using [FastQC](https://github.com/s-andrews/FastQC) version 0.11.9, and the results were saved in `results/FastQC_report`. Here is the command line: ```