For the detection of COVID-19 cases, nasal swab or saliva samples were tested using the RT-PCR assay (Japanese National Institute of Infectious Disease N2 with EAV)9 (link) at the reference laboratory (Kyoto University). All positive samples were subjected to viral genome analysis using the COVIDSeq Test (RUO version; Illumina, San Diego, CA) with the ARTIC V4.1 primer set and the NextSeq1000 platform (Illumina). The data were processed using DRAGEN COVID Lineage App version 3.5.8 (Illumina), and consensus sequences were generated using the SARS-CoV-2 reference genome (NC_045512). Genomes sequenced with a >90% breadth of coverage of the reference genome underwent lineage assignment using Pangolin version 4.0.6.10 (link) Phylogenetic analysis was performed using IQ-TREE multicore version 2.1.2 COVID-edition. The SARS-CoV-2 sequences obtained in this study are available in the GISAID database. The accession numbers are shown in Supplementary Dataset1.
Nextseq 1000 platform
Manufactured by Illumina
Sourced in Canada
The NextSeq 1000 is a next-generation sequencing platform designed for high-throughput and flexible sequencing applications. It employs sequencing-by-synthesis technology to generate sequencing data. The core function of the NextSeq 1000 is to perform DNA and RNA sequencing.
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Lab products found in correlation
3 protocols using nextseq 1000 platform
1
Detection and Genomic Analysis of COVID-19
2
Bacterial Whole-Genome Sequencing and Analysis
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Whole-genome sequencing of bacterial isolates was performed using the NextSeq 1000 platform (Illumina). The draft genome sequence was assembled using A5-miseq with Illumina short-read data. Gene annotation was performed using DFAST version 1.2.3 [33 (link)] using the following databases: DFAST default database, ResFinder database [34 (link)], Bacterial Antimicrobial Resistance Reference Gene (BARRG) database (PRJNA313047), and Virulence Factors Database [35 (link)]. Multilocus sequence typing (MLST) was performed using “mlst” program version 2.16.2 (Seemann T, mlst Github https://github.com/tseemann/mlst ) with PubMLST database (https://pubmlst.org/ ).
3
Whole Genome Sequencing of S. pyogenes
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For this study, whole genome sequencing of all clinical isolates (invasive and non-invasive) was performed by the UKHSA reference laboratory using the Illumina NextSeq 1000 platform with 100 base paired-end chemistry. Reads were trimmed to remove adaptor sequences and low-quality bases with Trimmomatic v0.3947 (link). Contamination was assessed based on Kraken248 (link) classification of reads mapped against a standard database for bacteria. Genomes with less than 90% of the reads mapped against S. pyogenes were excluded. Draught genomes were generated using SPAdes v3.15.449 (link). The assembly quality was assessed using QUAST v5.0.244 (link), and poor assemblies were filtered out if the genome size was higher than 2.1 Mbp and/or had more than 400 contigs. Genome annotation was performed with prokka v1.14.646 (link).
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