Selected article for: "host reference genome and pangolin host reference genome"
Author: Matthew C. Wong; Sara J. Javornik Cregeen; Nadim J. Ajami; Joseph F. Petrosino
Title: Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019
  • Document date: 2020_2_13
    • ID: dnxhtbxn_7
    Snippet: Sequences from each project were trimmed (minimum quality score 20 and minimum length 75bp) and filtered for Illumina adapter and PhiX presence using bbduk.sh v38.71 7 . Prior to analysis all sequences were filtered against a the relevant host reference genome (pangolin ManJav1.0, PRJNA256023 or bat mRhiFer1_v1.p, PRJNA489106) using bbmap.sh v38.71(k=15 and minid=0.9) 7 . After trimming and filtering, sequence reads were processed using VirMAP 5 .....
    Document: Sequences from each project were trimmed (minimum quality score 20 and minimum length 75bp) and filtered for Illumina adapter and PhiX presence using bbduk.sh v38.71 7 . Prior to analysis all sequences were filtered against a the relevant host reference genome (pangolin ManJav1.0, PRJNA256023 or bat mRhiFer1_v1.p, PRJNA489106) using bbmap.sh v38.71(k=15 and minid=0.9) 7 . After trimming and filtering, sequence reads were processed using VirMAP 5 to obtain and identify coronavirus genomes present in the viral metagenomic dataset. Two coronavirus genomes sharing high homology to nCoV-2019 were recovered from the pangolin dataset in two samples (SRR10168377 and SRR10168378).

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