Selected article for: "length read and read length"
Author: Jing Lu; Louis du Plessis; Zhe Liu; Verity Hill; Min Kang; Huifang Lin; Jiufeng Sun; Sarah Francois; Moritz U G Kraemer; Nuno R Faria; John T McCrone; Jinju Peng; Qianling Xiong; Runyu Yuan; Lilian Zeng; Pingping Zhou; Chuming Liang; Lina Yi; Jun Liu; Jianpeng Xiao; Jianxiong Hu; Tao Liu; Wenjun Ma; Wei Li; Juan Su; Huanying Zheng; Bo Peng; Shisong Fang; Wenzhe Su; Kuibiao Li; Ruilin Sun; Ru Bai; Xi Tang; Minfeng Liang; Josh Quick; Tie Song; Andrew Rambaut; Nick Loman; Jayna Raghwani; Oliver Pybus; Changwen Ke
Title: Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China
  • Document date: 2020_4_4
    • ID: ju9japd8_49
    Snippet: Reference-based assembly of the metagenomic raw data was performed as follows. Illumina adaptors were removed, and reads were filtered for quality (q30 threshold and read length >15nt) using Cutadapt 1.18 (Martin, 2011) . The mapping of cleaned reads was performed against GenBank reference strain MN908947.3 using Bowtie2 (Langmead and Salzberg, 2012) . Consensus sequences were generated using samtools 1.2 (Li et al., 2009) . Sites were called at .....
    Document: Reference-based assembly of the metagenomic raw data was performed as follows. Illumina adaptors were removed, and reads were filtered for quality (q30 threshold and read length >15nt) using Cutadapt 1.18 (Martin, 2011) . The mapping of cleaned reads was performed against GenBank reference strain MN908947.3 using Bowtie2 (Langmead and Salzberg, 2012) . Consensus sequences were generated using samtools 1.2 (Li et al., 2009) . Sites were called at depth>=3 if they matched the reference strain, or depth>=5 if they differed from the reference, otherwise sites were denoted N.

    Search related documents:
    Co phrase search for related documents
    • Consensus sequence and GenBank reference: 1, 2
    • Consensus sequence and GenBank reference strain: 1
    • Consensus sequence and reference strain: 1, 2
    • GenBank reference and reference strain: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
    • GenBank reference strain and reference strain: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10