LIQUORICE: Detect epigenetic signatures in cell-free DNA from liquid biopsies

Welcome to LIQUORICE’s documentation! You can navigate through the menu on the left to learn more about the tool. A very condensed overview follows below:


LIQUORICE is a bioinformatic command-line-tool and python package for bias correction and quantification of changes in sequencing coverage around regions of interest in cfDNA WGS datasets. LIQUORICE can be used to detect and quantify tissue or cancer-specific epigenetic signatures in liquid biopsies. The tool takes four different files as input:

  • a FASTA file of the reference genome

  • an indexed BAM file containing the aligned paired-end whole-genome sequencing reads of a liquid biopsy sample

  • a BIGWIG mappability file, available for download for hg19 and hg38 here

  • one or more BED files representing a set of regions of interest (such as DNase I hypersensitivity sites or enhancer regions specific for a tissue or tumor). Read more here.

You can install LIQUORICE like so (details):

# to install on Linux
conda create -n LIQUORICE -c bioconda -c conda-forge liquorice ray-core

# to activate the environment
conda activate LIQUORICE # or: 'source activate LIQUORICE' for older conda versions

You can test LIQUORICE on a small test dataset we provide by following the example below. Please note that the .bam and .bw file used in this example should only be used for testing purposes. They have been processed to keep the file size small.

# Set desired nr. of cpus

# download and unzip the reference genome and reference mappability file
gunzip hg38.p12.fa.gz

# download .bam file of a healthy control liquid biopsy sample (pre-processed to keep the size small)

# download .bed file for universally accessible DHSs

LIQUORICE --bamfile Ctrl_17_testdata.bam --refgenome_fasta "hg38.p12.fa" \
        --mappability_bigwig "" \
        --bedpathlist "universal_DHSs.bed" \
        --blacklist "hg38" --n_cpus "${N_CPUS}" --extend_to 15000

Indices and tables