RT Journal
A1 Jayasooriya, Kavindu
A1 Jenner, Sasha P.
A1 Marasinghe, Pasindu
A1 Senanayake, Udith
A1 Saadat, Hassaan
A1 Taubman, David
A1 Ragel, Roshan
A1 Gamaarachchi, Hasindu
A1 Deveson, Ira W.
T1 A new compression strategy to reduce the size of nanopore sequencing data
JF Genome Research 
JO Genome Research 
YR 2025 
FD July 01 
VO 35 
IS 7 
SP 1574 
OP 1582 
DO 10.1101/gr.280090.124 
UL http://genome.cshlp.org/content/35/7/1574.abstract 
AB Nanopore sequencing is an increasingly central tool for genomics. Despite rapid advances in the field, large data volumes and computational bottlenecks continue to pose major challenges. Here, we introduce ex-zd, a new data compression strategy that helps address the large size of raw signal data generated during nanopore experiments. Ex-zd encompasses both a lossless compression method, which modestly outperforms all current methods for nanopore signal data compression, and a ‘lossy’ method, which can be used to achieve additional savings. The latter component works by reducing the number of bits used to encode signal data. We show that the three least significant bits in signal data generated on instruments from Oxford Nanopore Technologies (ONT) predominantly encode noise. Their removal reduces file sizes by half without impacting downstream analyses, including basecalling and detection of modified DNA or RNA bases. Ex-zd compression saves hundreds of gigabytes on a single ONT sequencing experiment, thereby increasing the scalability, portability, and accessibility of nanopore sequencing.