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Project: chromosome Y assembly

This project repository contains a Snakemake workflow to produce whole-genome Verkko assemblies, and extract contigs that most likely represent the Y chromosome. The workflow requires HiFi and ONT reads to be executed, plus Illumina short reads for certain assembly evaluation tasks.

The input sample sheet is a simple tab-separated table listing sample name (sample) and (file system) location of read sets (hifi, ont and short if available). The sample sheet needs to be loaded as follows:

$ snakemake --config samples=PATH_TO_SAMPLE_SHEET [...]

Example sample sheet

Tool setup

The entire workflow uses Conda environments wherever possible to deploy software dependencies. A base environment containing Snakemake itself is defined in workflow/envs/run_env.yaml.

For software in development/prototype stage (Verkko and VerityMap), adaptations to the local infrastructure (Verkko) or building specific bugfix versions (VerityMap, see module workflow/envs/80_est_assm_errors.smk) is required, with the former not being automatable.

Plotting

The folder notebooks/ contains Jupyter notebooks used to plot various summary statistics of the generated assemblies. The notebooks contain a brief description documenting the necessary input files (produced by the Snakemake workflow).

Citation

In preparation