CSNMG: constructing sequence neighbourhood mapping graphs to compress FASTQ files

Shuhan Wang

doi:10.1117/12.2680153

16 June 2023 CSNMG: constructing sequence neighbourhood mapping graphs to compress FASTQ files

Shuhan Wang

Author Affiliations +

Proceedings Volume 12702, International Conference on Intelligent Systems, Communications, and Computer Networks (ISCCN 2023); 127022S (2023) https://doi.org/10.1117/12.2680153
Event: International Conference on Intelligent Systems, Communications, and Computer Networks (ISCCN 2023), 2023, Changsha, China

Abstract

With advances in sequencing technology, long-read sequences in single molecular sequencing (SMS) technologies have more structural variation and sequencing errors than short-read sequences in next-generation sequencing (NGS). Most of the current gene compression schemes have been developed for short read sequences, and further research is needed to develop more suitable compressors for long read sequences. We propose a reference-free compression scheme for FASTQ file based on the construction of d-neighbourhood mapping graph, and obtain better experimental results.

Citation Download Citation

Shuhan Wang "CSNMG: constructing sequence neighbourhood mapping graphs to compress FASTQ files", Proc. SPIE 12702, International Conference on Intelligent Systems, Communications, and Computer Networks (ISCCN 2023), 127022S (16 June 2023); https://doi.org/10.1117/12.2680153

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