A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data. Issue 2 (1st October 2020)

• Record Type: Journal Article
• Authors: Chen, Shifu; He, Changshou; Li, Yingqiang; Li, Zhicheng; Melançon, Charles E
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 2(2021)
• Page Start: 924
• Page End: 935
• Publication Date: 2020-10-01
• Subjects: SARS-CoV-2 -- viruses -- microorganisms -- identification -- k-mer; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbaa231
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction and other preprocessing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, Middle East respiratory syndrome and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv .