LongTREC presents:

Nanopore sequencers read DNA and RNA as long molecules pass through tiny pores, and they do it in real time. This makes “adaptive sampling” possible: while a molecule is being read, software checks its first part and decides in a fraction of a second whether to keep reading or reject it. It is like a librarian who skims the first lines of each book and only keeps those on the right topic. This lets researchers focus sequencing on the genes or regions they care about. However, developing and testing this kind of software usually requires real sequencing runs, which use costly materials and precious samples.

The authors present Icarust, a simulator that behaves like a real Nanopore sequencer. It imitates the instrument’s control software and generates realistic raw signal from any reference genome, for both small (MinION) and large (PromethION) devices. It supports current pore chemistries and RNA, and it responds to adaptive sampling decisions just as a real run would. Its output works with standard analysis tools.

Icarust gives the community a free, open-source testbed for designing real-time sequencing strategies without spending samples or reagents. This lowers costs and speeds up innovation in targeted long-read sequencing. Because it can also simulate RNA signal, it may help develop smarter approaches for long-read transcriptomics.

Read the full text here: https://doi.org/10.1093/bioinformatics/btae141