Reproducible genome size estimation from hifi reads

Run jellyfish followed by genomescope from hifi reads.

Dependendencies

• Singularity
• Nextflow
• pgonzale60/genokmer image

Installation

You can get the dependencies via conda

conda install -c bioconda nextflow singularity

At the moment the singularity image should be found under the $HOME directory.

cd $HOME
singularity pull docker://pgonzale60/genokmer

Usage

To execute the pipeline:

nextflow run pgonzale60/genokmer_hifi  --reads '/path/to/reads/*fasta'