WestGermanGenomeCenter

deepconsensus 1.2 snakemake pipeline

This snakemake-based workflow takes in a subreads.bam and results in a deepconsensus.fastq

• no methylation calls !

The metadata id of the subreads file needs to be: "m[numeric][numeric][numeric].subreads.bam"

Chunking (how many subjobs) and ccs min quality filter can be adjusted in the config.yaml

the checkpoint model for deepconsensus1.2 should be accessible like this: gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* ...