Selected article for: "quality score and read alignment"
Author: Ye, Fuqiang; Han, Yifang; Zhu, Juanjuan; Li, Peng; Zhang, Qi; Lin, Yanfeng; Wang, Taiwu; Lv, Heng; Wang, Changjun; Wang, Chunhui; Zhang, Jinhai
Title: First Identification of Human Adenovirus Subtype 21a in China With MinION and Illumina Sequencers
  • Document date: 2020_4_7
    • ID: 18b2foud_17
    Snippet: During MinION sequencing, Guppy embedded in MinKNOW (v3.3.2) performed the basecalling of raw signal event files to fastq reads. Reads with an average quality score ≥7 were labeled as "pass" files and were used for downstream analysis. Nanoplot (v1.22.0) (De Coster et al., 2018) was used to get an overview of the sequencing data including distributions of quality score and length. To calculate the percentages of reads belonging to the host, vir.....
    Document: During MinION sequencing, Guppy embedded in MinKNOW (v3.3.2) performed the basecalling of raw signal event files to fastq reads. Reads with an average quality score ≥7 were labeled as "pass" files and were used for downstream analysis. Nanoplot (v1.22.0) (De Coster et al., 2018) was used to get an overview of the sequencing data including distributions of quality score and length. To calculate the percentages of reads belonging to the host, virus, bacteria, and archaea at the level of superkingdom, we employed Minimap2 (v2.16) (Li, 2018) and BLASTN (v2.8.1) to align the reads against reference genomes downloaded from National Center for Biotechnology Information (NCBI) RefSeq database as of March 21, 2019, including the human genome (Grch38.p12), virus genomes (n = 8,588), bacteria genomes (n = 12,668), and archaea genomes (n = 283). The parameters of Minimap2 in aligning to human and viral genomes were "-ax map-ont -k 15" and "-ax map-ont -k 7, " respectively. Samtools (v1.9) (Li, 2011) was used to handle the sam or bam files to extract aligned or unaligned reads for next-step alignment. Read depth across a reference genome was obtained by the "samtools depth" function.

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