This repo recomputes intermediate alignments and consensus sequences from the study:
Seifert D, et al. (2016) A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations. Journal of Molecular Biology 428(1):238–250. doi:10.1016/j.jmb.2015.12.012
This study includes Illumina sequencing data deposited in the Sequence Read Archive and code for performing alignments and calling Primer ID consensus sequences, available from github. We have recomputed these intermediate alignment and consensus sequence results for use in other studies of HIV plasmid sequences, in particular for:
Measurement error and variant-calling in deep Illumina sequencing of HIV
The computed results are available from figshare at https://doi.org/10.6084/m9.figshare.6713132.v1.
Compiled Linux 64-bit binaries are available for all dependencies in the kantorlab Anaconda channel. The corresponding conda recipes are available from https://github.com/kantorlab/conda-recipes.
To use the packages, first install Anaconda 3. Then recreate the analysis environment with the command:
conda create -n primer-id-5vm -c kantorlab ampliconclipper fastx_toolkit picard prinseq scons=3.0.1.1
conda install -n primer-id-5vm -c bioconda sra-tools
conda install -n primer-id-5vm gcc_linux-64 gxx_linux-64 boost=1.65.1 gsl
source activate primer-id-5vm
All results can be recomputed by executing scons in the root directory of the repo.