Repository files navigation

This is repository contains Dynamic Mapping Simulator and supporting information for the paperK. 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 standardstatic mapping anditerative 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

• Python 3.3/3.4
• OCOCO
• RNFtools

Additional software for reports

• GNU Parallel
• LaTeX
• Inkscape
• Gnuplot 5

Environment installation:

conda create -y --name dymas \  -c bioconda \python==3.4 \snakemake samtools git cmake gnuplot ococo numpy biopython pysam==0.8.3

Environment activation:

source activate dymas

Installation of Python packages (in the activated environment)

pip install -r requirements.txt

0. Install all required software and activate the corresponding Conda environment.

source activate dymas

1. Remove computed data

make clean

2. Download reference genomes

make -C experiments/exp0*

3. Run experiments (this step will take several hours)

make -C experiments -j 10

4. Generate reports

make -C reports -j 10