MPD - Multiplex PCR Design

by Thomas Wingo and David Cutler

Citation

Please cite our paper if you use MPD in your work. Thanks.

Description

MPD is a program designed to automate creation of multiplex primer design written in C. The mpd_lessGreedy and mpd_moreGreedy binaries differ in which primer pool they choose to start with for pool creation. Either binary can be used as stand-alone or in conjunction with the MPD perl package.

Installation

• Clone the repository
• Make with make all
• Binaries will be compiled and saved to the build directory

Required files

• You will need a hashed copy of the genome to run the primer software.
• Instructions below show how you can create one yourself. A prebuild hg38 genome with flat dbSnp files is available from this repository. It may be cloned like so, git clone https://bitbucket.org/wingolab/mpd-dat.git.

Build Hashed Genome

• Download the genome of interest as a fasta file
• Use bin/run_index.pl, which creates a sh script to run index_genome
  • You'll need to install these perl packages to use this script: Path::Tiny, Data::Dump, and Getopt::Long, which can be installed using cpanm like so cpanm Path::Tiny Data::Dump Getopt::Long.

Flat dbSnp

• These can be obtained from this this repository, which were prepared from dbSNP version 140.
• To create your own flat snp file set based on criteria of your own devising, each line should contain tab-delimited fields of the following:

name numberOfReporters chrom position MinorAlleleFrequency allele1/allele2

• The numberOfReporters field is no longer used but retained for backwards compatibility.
• Prepare a sdx file that contains the number of chromsome files to include as the 1st line and then a list of the names of all chromosome files. On the command line you might try: ls -1 *.line | wc -l > db_flat.sdx; ls -1 >> db_flat.sdx. Note that the sdx should be in the same order that the chromsomes are in for the indexed genome. See the genome's sdx file (e.g., cat hg38.d14.sdx) to see the order.

Run mpd

• The easiest way of using MPD is to use the Perl pacakge MPD, but either mpd_lessGreedy and mpd_moreGreedy binaries may be executed from the command line interactively.