Selected article for: "low quality and reference genome"
Author: Xianding Deng; Wei Gu; Scot Federman; Louis Du Plessis; Oliver Pybus; Nuno Faria; Candace Wang; Guixia Yu; Chao-Yang Pan; Hugo Guevara; Alicia Sotomayor-Gonzalez; Kelsey Zorn; Allan Gopez; Venice Servellita; Elaine Hsu; Steve Miller; Trevor Bedford; Alexander Greninger; Pavitra Roychoudhury; Michael Famulare; Helen Y Chu; Jay Shendure; Lea Starita; Catie Anderson; Karthik Gangavarapu; Mark Zeller; Emily Spencer; Kristian Andersen; Duncan MacCannell; Suxiang Tong; Gregory Armstrong; Clinton Paden; Yan Li; Ying Zhang; Scott Morrow; Matthew Willis; Bela Matyas; Sundari Mase; Olivia Kasirye; Maggie Park; Curtis Chan; Alexander Yu; Shua Chai; Elsa Villarino; Brandon Bonin; Debra Wadford; Charles Y Chiu
Title: A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage
  • Document date: 2020_3_30
    • ID: cbc98t7x_31
    Snippet: Raw reads were first screened via BLASTn (BLAST+ package 2.9.0) (23) for alignment to reference strain NC_045512. They were then aligned to the reference with LASTZ version 1.04.03. SARS-CoV-2 reads were trimmed using Geneious version 11.1.3 by removal of 13 nucleotides (nt) (the length of the MSSPE primer) and low-quality reads from the ends, followed by removal of duplicate reads. Trimmed reads were mapped to reference genome NC_045512 in Genei.....
    Document: Raw reads were first screened via BLASTn (BLAST+ package 2.9.0) (23) for alignment to reference strain NC_045512. They were then aligned to the reference with LASTZ version 1.04.03. SARS-CoV-2 reads were trimmed using Geneious version 11.1.3 by removal of 13 nucleotides (nt) (the length of the MSSPE primer) and low-quality reads from the ends, followed by removal of duplicate reads. Trimmed reads were mapped to reference genome NC_045512 in Geneious with no gaps allowed and a maximum of 5% mismatches per read. The assembled contig was then manually annotated, and a consensus genome was generated using a majority threshold criterion.

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