SARS-Cov-2文献阅读
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https://www.frontiersin.org/articles/10.3389/fgene.2021.620009/full
Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing
对血液感染的肺炎克雷伯菌进行的检测 分析了物种及其耐药性和毒力
Albacore v2.2.6
Porechop v0.2.3
quality control was run through Pauvre v0.1.86
filtered using NanoFilt v2.2.0
Canu v1.6 and nanopolish v0.10.16 were used for nanopore long-read-only assembly and polishing
Unicycler v0.4.5 was also used for hybrid assembly of Illumina reads and nanopore reads
Species identification was performed by Kraken Software v2.0.8-beta 这个文献用Kraken鉴定了nanopore物种
CARD database through RGI v4.2.2 (Resistance Gene Identifier)
Real-time analyses were performed by aligning MinION fastq reads to CARD database v3.0.0 through blastn (blast+, v2.2.28), seeking results with identity ≥80%, hit length ≥100 bp, and gene coverage ≥70%.
