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 pre-processing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid 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, MERS, and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.
ABSTRACT
Based on international framework of rehabilitation, this paper summarized the theories and practice of rehabilitation in Shen-zhen. An inclusive rehabilitation model had been established in Shenzhen in light of international concepts of rehabilitation, in which the functions of medical rehabilitation, education, employment, assistive technology, care, right protection, accessible environment and culture had been integrated. The comprehensive services had been provided through this model and the target of inclusive development had been re-alized.
