Selected article for: "mapping read and sequence read"
Author: Peña, José; Chen-Harris, Haiyin; Allen, Jonathan E.; Hwang, Mona; Elsheikh, Maher; Mabery, Shalini; Bielefeldt-Ohmann, Helle; Zemla, Adam T.; Bowen, Richard A.; Borucki, Monica K.
Title: Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage
  • Document date: 2016_4_9
    • ID: z7f720dj_26
    Snippet: Read mapping and rare variant detection was performed as described previously in Chen-Harris et al. (2013) and Borucki et al. (2013) . The open source read mapping software SHRiMP2 (David et al. 2011) , was used to map reads using GenBank SeV Z strain (GI: 546225824) as a reference sequence which was shown to have high read mapping sensitivity (Holtgrewe et al. 2011) and was chosen for the tool's ability to map as many reads as possible in the fa.....
    Document: Read mapping and rare variant detection was performed as described previously in Chen-Harris et al. (2013) and Borucki et al. (2013) . The open source read mapping software SHRiMP2 (David et al. 2011) , was used to map reads using GenBank SeV Z strain (GI: 546225824) as a reference sequence which was shown to have high read mapping sensitivity (Holtgrewe et al. 2011) and was chosen for the tool's ability to map as many reads as possible in the face of individual errors within each read. To differentiate rare variants from sequencing errors, methodologies were developed to measure and control for sequencing and PCR errors and described previously in Chen-Harris et al. (2013) . Error models have been refined for Illumina sequencing platform to allow detection of ultra-rare mutations within the viral population (Chen-Harris et al. 2013; Borucki et al. 2013) . The Illumina reads were submitted to the GenBank Sequence Read Archive (BioProject PRJNA314501).

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