Alignment of Viral Genomes Using Mosaik

The reference genomes chosen for aligning the input reads are NC001475 (NCBI accession number) for Dengue, NC009942 for West Nile, and a modified version of the HXB2 reference K03455 for HIV. The HIV reference genome is a subsequence of HXB2 (from 779bp to 9551bp) and is corrected for a frame-shift and a premature stop codon (available upon request). The target regions for analyses consist of the complete CDS of each reference genome, which corresponds to positions 95-10267 for Dengue, 97-10398 for West Nile and 12-8638 for HIV.
Read alignment to reference genome or assemblies are carried out using Mosaik v1.1.0013 (
http://bioinformatics.bc.edu/marthlab/Mosaik), with parameter setting “st = illumina, hs = 10, act = 15, bw = 29, mmp = 0.25 and minp = 0.25”.

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Yang X., Charlebois P., Gnerre S., Coole M.G., Lennon N.J., Levin J.Z., Qu J., Ryan E.M., Zody M.C, & Henn M.R. (2012). De novo assembly of highly diverse viral populations. BMC Genomics, 13, 475.

Publication 2012

Dengue Frame Genome Premature stop codon

Corresponding Organization :

Other organizations : Broad Institute

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Variable analysis

independent variables

Reference genomes chosen for aligning the input reads: NC001475 (NCBI accession number) for Dengue, NC009942 for West Nile, and a modified version of the HXB2 reference K03455 for HIV

dependent variables

Read alignment to reference genome or assemblies

control variables

The HIV reference genome is a subsequence of HXB2 (from 779bp to 9551bp) and is corrected for a frame-shift and a premature stop codon
The target regions for analyses consist of the complete CDS of each reference genome, which corresponds to positions 95-10267 for Dengue, 97-10398 for West Nile and 12-8638 for HIV
Read alignment to reference genome or assemblies are carried out using Mosaik v1.1.0013 with parameter setting "st = illumina, hs = 10, act = 15, bw = 29, mmp = 0.25 and minp = 0.25"

controls

There are no explicit positive or negative controls mentioned in the provided information.

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