Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language

PeerJ

article

Daniel Liu¹ 

[1] Torrey Pines High School;Department of Psychiatry, University of California

关键词: Demultiplexing;    Adapter trimming;    String matching;    FASTQ;    Domain-specific language;   

DOI  :  10.7717/peerj.7170

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Next-generation sequencing technologies create large, multiplexed DNA sequences that require preprocessing before any further analysis. Part of this preprocessing includes demultiplexing and trimming sequences. Although there are many existing tools that can handle these preprocessing steps, they cannot be easily extended to new sequence schematics when new pipelines are developed. We present Fuzzysplit, a tool that relies on a simple declarative language to describe the schematics of sequences, which makes it incredibly adaptable to different use cases. In this paper, we explain the matching algorithms behind Fuzzysplit and we provide a preliminary comparison of its performance with other well-established tools. Overall, we find that its matching accuracy is comparable to previous tools.

【 授权许可】

CC BY