make artificial mate pairs from long sequences for scaffolding
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matemaker has not been tested extensively and is being actively developed. Please use with caution. I appreciate hearing about your experience with the program.

matemaker will generate a pair of fastq files (left and right) that consist of artificial mate-pairs generated from one or more sequences sent in as input. It is intended to scaffold an optimal assembly with suboptimal assemblies. The generated matepairs are in the same orientation as illumina matepair sequencing, and can be used without modification as input to any scaffolding software that accepts illumina mate-pairs (e.g., SSPACE). Quality scores are all set to unknown (represented by the character 'B').

I recommend running the program multiple times with an array of insert sizes. See examples.


AVAILABILITY (click the "Download ZIP" button at the bottom of the right column).


General system tools:

Additional package


To install matemaker and documentation, type the following:

perl Makefile.PL
sudo make install

If you do not have permission to install to the system see the following:


matemaker --assembly=ASSEMBLY.fa --out=PREFIX


In the examples directory there are 2 files: Hsap.chr22.opt.fa - (N50: 5000000) Human Chromosome 22 divided into chunks of size 5000000

  Hsap.chr22.subopt.fa - (N50: 1000000)
  Human Chromosome 22 divided into chunks of size 1000000
  The first 25000000 NTs (of which all were N) were removed to create
  an offset of breakpoints with Hsap.chr22.opt.fa

To create matepairs try:

  matemaker --assembly=Hsap.chr22.subopt.fa --insertsize=2000 --out=chr22.2000
  matemaker --assembly=Hsap.chr22.subopt.fa --insertsize=5000 --out=chr22.5000
  matemaker --assembly=Hsap.chr22.subopt.fa --insertsize=10000 --out=chr22.10000

The resulting files are:

  chr22.2000.A.fq,  chr22.2000.B.fq

  chr22.5000.A.fq,  chr22.5000.B.fq

  chr22.10000.A.fq, chr22.10000.B.fq

These can be used as input to a scaffolding software (e.g., SSPACE) to scaffold the optimal assembly:



Documentation is embedded inside of matemaker in POD format and can be viewed by running any of the following:

    matemaker --help
    perldoc matemaker
    man matemaker  # available after installation


Copyright (C) 2015 Joseph F. Ryan

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.

You should have received a copy of the GNU General Public License along with this program in the file LICENSE. If not, see