Workflows

scRNAseq

Single-cell RNA sequencing workflow. This workflow is based on a setup by Åsa Björklund. See repaper/Treutlein_2014 for an example. The rulegraph is shown below.

ATAC-seq

Implementation of workflow in Buenrostro et al 2013 for ATAC-seq. See repaper/Buenrostro_2013 for an example. The rulegraph is shown below.

methylseq

Bisulfite-sequencing analysis workflow.

variation

Run GATK best practice pipeline for variant calling.

halo

To be reimplemented from biomake.

BROAD_rnaseq