A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data.

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 dir

SUBMITTER: Chen S 

PROVIDER: S-EPMC7543257 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature