Figure 1.

(A) Existing TKSM modules and utilities alongside their high-level descriptions. TKSM is designed with modularity in mind; the user can specify a simulation pipeline of their choosing by chaining any number of TKSM modules including the possibility of using the same module multiple times. (B) Typical RNA-seq simulation pipeline that imitates Trans-Nanosim’s workflow. (C) Single-cell long-read simulation pipeline. The pipeline makes use of the Filtering and Merging modules to add the short-read Illumina adapter and 10× Genomics cellular barcodes only to molecules that have a tag indicating that they should have a cellular barcode.