Download and Installation

Author: SeekGene

Time: 3 min

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Updated: 2026-10-13

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scMethyl + RNA-seq Download

Clone the Repository

git clone https://github.com/seekgene/SeekSoulMethyl.git
cd SeekSoulMethyl

Create the Conda Environment

For users in China:

conda env create -n seeksoulmethyl -f conda_dependencies.zh.yml
conda activate seeksoulmethyl

For international users:

conda env create -n seeksoulmethyl -f conda_dependencies.yml
conda activate seeksoulmethyl

Install the Package

cd dependence
pip install . \
  simpleqc/target/wheels/simpleqc-0.1.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl \
  search-pattern/target/wheels/search_pattern-0.1.0-py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.whl
cd ..

Install Modified Dependencies

SeekSoul™ Methyl Tools relies on customized versions of Bismark and ALLCools:

• Bismark: adds CB and UR tags to BAM records
• ALLCools: supports UR-based UMI correction and methylation quantification

conda activate seeksoulmethyl

# Install custom ALLCools
git clone https://github.com/seekgene/ALLCools.git
pip install ./ALLCools
rm -rf ./ALLCools

# Install custom Bismark
git clone https://github.com/seekgene/Bismark.git
bin_path=$(dirname `which python`)
cp -r ./Bismark/* $bin_path/
chmod +x $bin_path/bismark*
chmod +x $bin_path/deduplicate_bismark
rm -rf ./Bismark

Repository Structure

After cloning, the key Nextflow entry points and modules are:

• nf/main.nf: Top-level entry. Select sub-workflow via --workflow (rna_met, methy_only, force_cell).
• nf/subworkflows/: Workflow definitions:
  • rna_met/main.nf: Transcriptome + methylation end-to-end processing.
  • met_only/main.nf: Methylation-only workflow.
  • forcecell/main.nf: Force-cell workflow (recomputes/updates results using previous outputs).
• nf/modules/: Step-wise process modules:
  • step1.nf: preprocessing, QC, barcode extraction, transcriptome analysis.
  • step2.nf: Bismark alignment and BAM sorting.
  • step3.nf: per-cell BAM splitting, ALLC generation/merge, multi-scale datasets.
  • step4.nf: summaries, dimensionality reduction, joint report.
  • utils.nf: helpers for methylation-only workflow (reads counting and cell estimation).
• nf/bin/: Helper scripts and resources (e.g., barcode whitelists).
• nf/nextflow.config: Executors and resource configuration.
• nf/nextflow_schema.json: Pipeline parameter schema.
• sc_methy_workflow.sh: Shell script to run the dual-omics analysis pipeline.

Download the Reference Database

Prebuilt reference archives are available for common species:

# Human reference genome (GRCh38)
wget -c -O human-reference-GRCh38.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/human-reference-GRCh38.tar.gz"
wget -c -O human-reference-GRCh38.tar.gz.md5 "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/human-reference-GRCh38.tar.gz.md5"

# Mouse reference genome (GRCm39)
wget -c -O mouse-reference-GRCm39.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/mouse-reference-GRCm39.tar.gz"
wget -c -O mouse-reference-GRCm39.tar.gz.md5 "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/mouse-reference-GRCm39.tar.gz.md5"

# Extract archives
tar -xzf human-reference-GRCh38.tar.gz
tar -xzf mouse-reference-GRCm39.tar.gz

If you need to build a custom reference database, see:

• Reference genome database guide
• Full build tutorial

Download Test Data

For downloading demo data, please refer to the Datasets document.

Demo Resources

For complete demo datasets and downloadable result bundles, see the supplementary documents:

• Cell line demo datasets