And of course, this work would not have been possible without the funding and institutional support of @SFU_CompSci @UBC_CS @VanProstateCtr @UBCUrology @SFUMath @NSERC_CRSNG @HlthResearchBC

Hope you all give TKSM a try and find it useful for simulating your long-read experiments!

All of this is packaged into a neat package that comes with a handy Snakefile to run your simulation configs (including full UNIX piping support!). And the insulation of each module means that you can write your own TKSM module! Here is a list of currently implemented modules:

These simulation pipelines can be more complex, with branches defined as their own linear pipelines! For example here is a scRNA-seq experiment that is made possbile by TSKM config:

This design allows the user to define arbitrary simulation pipelines using easy-to-write YAML configs. For example, here is a simple bulk RNA-seq long-read pipeline and its corresponding YAML config:

TKSM is a modular, easy-to-customize, and fast long-read simulator. Our design philosophy in TKSM is: 1. Each library prep step will be targeted by a TKSM module 2. The I/O of each core module is a description of nuclueic molecules that (eventually) will be reads

Our latest manuscript that's spearheaded by @fkaraoglan_cs and @baraaorabi (with the co-supervision of Cedric Chauve and collaboration of @RyanFlannigan00) is out! We are delighted for TKSM to say Hello World! 👋 💻: github.com/vpc-ccg/tksm 📄: biorxiv.org/content/10.1101/…