This is repository contains Dynamic Mapping Simulator and supporting information for the paper K. Břinda, V. Boeva, G. Kucherov: Dynamic read mapping and online consensus calling for better variant detection (arXiv:1605.09070).
Dynamic mapping is mapping to a reference, which is continuously corrected according to alignments computed so far. Dynamic Mapping Simulator is a pipeline to simulate dynamic mapping using existing software to evaluate its benefits in comparison to standard static mapping and iterative referencing. For more details, see the paper.
Scheme of the simulation pipeline:
Reads are taken in the following way:
SM = static mapping, DM = dynamic mapping without remapping, DM-remap = dynamic mapping with remapping, IR = iterative referencing
- docs - supplementary materials (S1 and S2 files)
- dymas - Dynamic Mapping Simulator (Python package)
- experiments - all runs of all experiments
- reports - generated reports
Experiments
Additional software for reports
- GNU Parallel
- LaTeX
- Inkscape
- Gnuplot 5
Recommended way of installation using Anaconda
Environment installation:
conda create -y --name dymas \
-c bioconda \
python==3.4 \
snakemake samtools git cmake gnuplot ococo numpy biopython pysam==0.8.3Environment activation:
source activate dymasInstallation of Python packages (in the activated environment)
pip install -r requirements.txt- Install all required software and activate the corresponding Conda environment.
source activate dymas- Remove computed data
make clean- Download reference genomes
make -C experiments/exp0*- Run experiments (this step will take several hours)
make -C experiments -j 10- Generate reports
make -C reports -j 10