TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.

ABSTRACT:

Motivation

Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle various transcriptomic sequencing tasks (e.g. isoform and gene fusion detection). However, the lack of abundant gold-standard datasets hinders the benchmarking of such tools. Therefore, the simulation of LR sequencing is an important and practical alternative. While the existing LR simulators aim to imitate the sequencing machine noise and to target specific library protocols, they lack some important library preparation steps (e.g. PCR) and are difficult to modify to new and changing library preparation techniques (e.g. single-cell LRs).

Results

We present TKSM, a modular and scalable LR simulator, de

SUBMITTER: Karaoglanoglu F 

PROVIDER: S-EPMC10868325 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature