Selected article for: "minimum quality and sequence analysis"
Author: Gage Kahl Moreno; Katarina M Braun; Peter J Halfmann; Trent M Prall; Kasen K Riemersma; Amelia K Haj; Joseph Lalli; Kelsey R Florek; Thomas C Friedrich; Yoshihiro Kawaoka; David H O'Connor
Title: Limited SARS-CoV-2 diversity within hosts and following passage in cell culture
  • Document date: 2020_4_20
    • ID: izu5x2d4_12
    Snippet: Illumina sequence data analysis -quality filtering and variant calling 362 FASTQ files were initially processed using custom bioinformatic pipelines, available with 363 instructions for use at the GitHub repository accompanying this manuscript 364 https://github.com/katarinabraun/SARSCoV2_passage_MS. Briefly, read ends were trimmed to 365 achieve an average read quality score of Q30 and a minimum read length of 100 bases using 366 The copyright h.....
    Document: Illumina sequence data analysis -quality filtering and variant calling 362 FASTQ files were initially processed using custom bioinformatic pipelines, available with 363 instructions for use at the GitHub repository accompanying this manuscript 364 https://github.com/katarinabraun/SARSCoV2_passage_MS. Briefly, read ends were trimmed to 365 achieve an average read quality score of Q30 and a minimum read length of 100 bases using 366 The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.051011 doi: bioRxiv preprint SNPGenie adapts the Nei and Gojobori method of estimating nucleotide diversity (π), and its 384 synonymous (π S ) and nonsynonymous (π N ) partitions from next-generation sequencing data 385 [31] . As most random nonsynonymous mutations are likely to be disadvantageous, we expect 386 π N = π S indicates neutrality suggesting that allele frequencies are determined primarily by 387 genetic drift. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.051011 doi: bioRxiv preprint

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