This is the ENCODE-DCC RNA-sequencing pipeline. The scope of the pipeline is to align reads, generate signal tracks, and quantify genes and isoforms.

This benchmarking workflow that can be used to assess performance of germline variant calling pipelines based on testing with GIAB samples.

Variant calling for long reads - utilizes PEPPER for SNP calling, Margin for haplotyping and phasing, and DeepVariant for genotype calling

This benchmarking workflow is used to assess performance of germline variant calling pipelines based on testing with GIAB samples.