Reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach.

ABSTRACT: The amount of data produced by genome sequencing experiments has been growing rapidly over the past several years, making compression important for efficient storage, transfer and analysis of the data. In recent years, nanopore sequencing technologies have seen increasing adoption since they are portable, real-time and provide long reads. However, there has been limited progress on compression of nanopore sequencing reads obtained in FASTQ files since most existing tools are either general-purpose or specialized for short read data. We present NanoSpring, a reference-free compressor for nanopore sequencing reads, relying on an approximate assembly approach. We evaluate NanoSpring on a variety of datasets including bacterial, metagenomic, plant, animal, and human whole genome data. For rece

SUBMITTER: Meng Q 

PROVIDER: S-EPMC9902536 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature