Reporting N‐stretches in the reference

Reporting N-stretches in the reference

CIEVaD provides an optional flag to report 'N'-nucleotide stretches in the reference genome. Via the parameter report_nstretches the reporting can be activated and, consequentially, CIEVaD generates an additional histogram (PNG) and BED file containing the genomic locations of the N-stretches.

From the command line interface this can be activated e.g. via

nextflow run hap.nf -profile local,conda --reference <myRef> --report_nstretches

This run command will produce the N-stretches report files for the <myRef> reference.