PARamrfinder

PARamrfinder is a high efficient, parallel application to predict allele-specific DNA methylation (ASM) in mammals in the absence of SNP data. It is based on the work of Fang F, Hodges E, Molaro A, Dean MD, Hannon GJ and Smith AD, amrfinder, and it has been fully optimized to reduce its runtime from days to less than 15 minutes.

Prerequisites

Before starting the installation, please confirm that the following software is available in your system. Particular versions using during development are shown.

• GCC v8.3.0
• GSL v2.6
• Zlib v1.2.11
• HTSlib v1.13
• CMake v3.28.1
• MPI compiler with support for OpenMP:
  • OpenMPI v3.1.4
• Git (Optional)

Different versions of the software may work but they have not been tested.

Compilation

If the requirements are met, Fiuncho can be configured and built with the following commands:

mkdir build
cd build
cmake ..
make

Optionally, you can test the correctness of the gererated program with the command:

make test

Execution

PARamrfinder must be executed with MPI execution commands (mpiexec (standard) or mpirun).Therefore, the tool can be executed using the following command from the root folder of the proyect:

mpiexec -n <numProcs> ./bin/PARamrfinder [OPTIONS] <epireads>

when numProcs is the number of MPI processes to execute, and options is a list of the following arguments:

• -o, -output output file
• -c, -chrom genome sequence file/directory (REQUIRED)
• -i, -itr max iterations
• -w, -window size of sliding window
• -m, -min-cov min coverage per cpg to test windows
• -g, -gap min allowed gap between amrs (in bp)
• -C, -crit critical p-value cutoff (default: 0.01)
• -t, -threads OpenMP threads on each process
• -f, -nofdr omits FDR multiple testing correction
• -h, -pvals adjusts p-values using Hochberg step-up
• -b, -bic use BIC to compare models
• -v, -verbose print more run info
• -P, -progress print progress info
• -a, -assert_individual_chroms asserts that each chrom comes in a separate file

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.