Sync paired-end FASTA/Q files and keep singleton reads
Clone or download
Latest commit e1435ad Mar 7, 2017


Sync paired-end FASTA/Q files and keep singleton reads

Build Status GitHub version


There is a standalone script in the 'scripts' directory that has no dependencies and will work with Perl version 5.6 or newer. This script has fewer features (mainly, it lacks the indexing function for working with large data) than the main application but it may be useful in an environment where installing libraries is not convenient. Obtaining this version can be done with curl:

curl -sL > pairfq_lite

You can then make the script executable and check the usage:

chmod +x pairfq_lite
./pairfq_lite -h

Alternatively, you can use this version without storing it locally.

curl -sL | perl -

The above command will show the options. To see a specific subcommand menu, for example the makepairs command, just type that subcommand with no options.

curl -sL | perl - makepairs

For a full explanation of all commands, please see the Support and Documenation section below.


The following command will install Pairfq (note that this requires git):

curl -sL | perl - git://

Alternatively, download the latest release and run the following command in the top directory:

perl Makefile.PL

If any Perl dependencies are listed after running this command, install them through the CPAN shell or any method you like (see the installing dependencies page for instructions). Then build and install the package.

perl Makefile.PL
make test
make install

The last command is optional, you can put the program in a custom location or use it in place.


See the Pairfq wiki for examples with each method.


After installation, you can find documentation for Pairfq with the perldoc command.

perldoc pairfq

The documentation can also be accessed by specifying the manual option with pairfq -m or pairfq --man. The pairfq program will also print a diagnostic help message when executed with no arguments. In addition, there is extensive documentation on the Pairfq wiki online.


Report any issues or feature requests at the Pairfq issue tracker.


This project uses the readfq library written by Heng Li. The readfq code has been modified for error handling and to parse the comment line in the Casava header.


The MIT License should included with the project. If not, it can be found at:

Copyright (C) 2013-2016 S. Evan Staton