Install

git clone https://github.com/liushoucheng/SPART.git

cd SPART

conda env create -f SPART.yaml

conda activate spart

Dependencies

List of tools assumed loadable or accessible with no path are:

• Bionano DLS map

• HiC-Pro v3.1.0

• _submit_telomere.sh

• Medaka

• racon

• hisat2

• DeepVariant v1.5.0-gpu

• PEPPER-Margin-DeepVariant v0.8-gpu

• hap.py v0.3.15

• vcf_merge_t2t.py

Running pipeline with snakemake

Exclude Verkko,Bionano DLS Map,Telomere determination and patch,Centromeric region analysis,Variant calls and Evaluation

sed -i “s#^ SPART_PATH# ${PWD}#g” conf_ck.yaml

HiC_enzyme=” GATC”

sed -i “s#^ hic_sca_enzyme# ${HiC_enzyme}#g” conf_ck.yaml

HiC_ligation_site=” GATCGATC”

sed -i “s#^ hic_sca_ligation_site# ${HiC_ligation_site}#g” conf_ck.yaml

snakemake -s SPART.py –cluster-config clust.json –configfile conf_ck.yaml –cluster ‘{cluster.account}’ –jobs $threads –rerun-incomplete –restart-times 1 -np –rulegraph |dot -Tpng > rule.png

configfile:The config file can be used to define a dictionary of configuration parameters and their values.

cluster-config:A JSON or YAML file that defines the wildcards used in ‘cluster’for specific rules.

Output files

please see the complete documentation.