Next-generation sequencing-based tools or nanopore-based tools: which is more suitable for short tandem repeats genotyping of nanopore sequencing?

Motivation: Short tandem repeats (STRs) are widely recognized as critical genetic markers for individual identification. Nanopore sequencing technology holds promise as an effective tool for onsite STR detection owing to its portability. Initially, low sequencing quality led to the development of various genotyping tools specifically tailored for nanopore data. However, recent advancements in nanopore sequencing quality suggest that tools designed for next-generation sequencing (NGS) may be more suitable for analyzing nanopore data than those specifically developed for nanopore sequencing.

Results: We selected two sequencing platforms, MinION Mk1C, and PolySeqOne, to generate sequencing data from 61 unrelated individual samples. Samples were amplified using a custom NanoSTR panel that included 31 autosomal STRs (A-STRs) and 31 Y chromosomal STRs (Y-STRs). Sequencing data were analyzed using four distinct tools: NASTRA, STRspy, STRinNGS, and STRait Razor. Our findings indicated that STRinNGS showed greater accuracy for both A-STRs and Y-STRs, enabling the accurate detection of a broad range of STRs. Compared with STRinNGS, NASTRA exhibited greater STR depth and featured more non-integer stutters. Therefore, in practical applications, STRinNGS demonstrates high reliability in genotyping.

Availability and implementation: NASTRA, STRspy, STRinNGS and STRait Razor, which can be accessed via the following links: https://github.com/renzilin/NASTRA, https://github.com/unique379r/strspy, https://bitbucket.org/rirgabiss/strinngs/src/master, and https://github.com/Ahhgust/STRaitRazor, respectively. The commands during process are provided as requested by the corresponding author.