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Genomes Analysis Made Easy
This repository contains a scalable, user-friendly pipeline for standardised, parallel analysis of genomes being developed as part of BGE+ and building upon lessons learned from ERGA and GEP2.
Data is entered via a simple table, and configuration is managed through a tidy control panel. GAME uses a modern Snakemake version with containers and can run on a server/cluster (SLURM) or a local computer.
Please cite: in preparation
Conda*Apptainer
*(or you could have the packages listed in the install.yml, in addition to Apptainer/Singularity, installed in your PATH)
• download assemblies & reads (or use the ones in your local storage)
• trim/filter/qc reads (paired-end, 10x, HiFi, ONT), plus QC reports
• produce a quick QC report to check the reference assembly
• de novo masking with RepeatModeler/Masker (or use your bed masking or extract softmasked from reference)
• map reads (paired-end, 10x, HiFi, ONT) with dynamic merging, plus QC reports and sex inference
• variant calling with DeepVariant or GATK, plus Joint Genotyping with GLnexus
• apply tags for flexible downstream soft filtering, plus QC reports
• check relatedness and LD prunning tagging, plus QC reports
• analyse heterozygosity and ROH (currently adding functionalities. Coming with next version bump!)
• generate PSMC analysis, plots and diagnostics (currently adding other demgraphic inference methods, like GONE, etc. Coming with further version bump!)
• more analysis coming with further version bumps! (Fst, PCA, admixture, structure...)