SiftDx: A clinical metagenomics pipeline for sifting through complex sequencing data to detect pathogens with precision
Please follow the guide in the
Full pipeline in DNA/RNA mode, just swap out the --na DNA in the code below to --na RNA
nextflow run main.nf -resume --na DNA --r1 PATH_TO_R1 --r2 PATH_TO_R2 --output PATH_TO_OUTPUT -with-trace
Full pipeline in RNA mode with ERCC controls, if you use MetaSequins for DNA spike-ins, use the --sequins flag instead
nextflow run main.nf -resume --na RNA --r1 PATH_TO_R1 --r2 PATH_TO_R2 --output PATH_TO_OUTPUT -with-trace --ercc
If you have a negative control, we'd advise you run the pipeline on it first using any of the above commands then run your sample with the negative control using the following.
nextflow run main.nf -resume --na RNA --r1 PATH_TO_R1 --r2 PATH_TO_R2 --output PATH_TO_OUTPUT -with-trace --ndata PATH_TO_NEGATIVE
Note: the PATH_TO_NEGATIVE is the path to the output, rather than the work directory
- A preprocessing only mode