SYNOPSIS

'fqgrep' is an approximate sequence pattern matcher for FASTQ/FASTA files. One can think of it as being a grep (http://en.wikipedia.org/wiki/Grep) and agrep (http://en.wikipedia.org/wiki/Agrep) like tool optimized for FASTQ (http://en.wikipedia.org/wiki/FASTQ_format) and FASTA (http://en.wikipedia.org/wiki/FASTA_format) files. It can work directly on both compressed and uncompressed file types.

Below is the help message via ('fqgrep -h') describing its usage:

Usage: fqgrep [options] -p <fastq_or_fasta_files> -h This help message -V Program and version information -p <STRING> Pattern of interest to grep [REQUIRED] -v Invert match - show only sequences that DO NOT match the pattern -a Show all records irregardless of match status Useful in conjunction with the -r option; when one would like to do further post-processing of the match data -c Highlight matching string with color -f Output matches in FASTA format -r Output matches in detailed stats report format -b <STRING> Delimiter string to separate columns in detailed stats report [Default: '\t'] -m <INT> Total number of mismatches to at most allow for in search pattern [Default: 0] -s <INT> Max threshold of substitution mismatches to allow for in search pattern [Default: unlimited] -i <INT> Max threshold of insertion mismatches to allow for in search pattern [Default: unlimited] -d <INT> Max threshold of deletion mismatches to allow for in search pattern [Default: unlimited] -S <INT> Cost of base substitutions in obtaining approximate match [Default: 1] -I <INT> Cost of base insertions in obtaining approximate match [Default: 1] -D <INT> Cost of base deletions in obtaining approximate match [Default: 1] -e Force tre regexp engine usage -C Display only a total count of matches (per input FASTQ/FASTA file) -o <out_file> Desired output file. If not specified, defaults to stdout

PREREQUISITES

"fqgrep" depends upon the following libraries:

• TRE Regular Expression Library (TRE) [http://laurikari.net/tre/] version 0.8.0.
• zlib [http://www.zlib.net]

They will need to be available on your system before fqgrep can be installed.

TRE
===

    On Ubuntu (or any other Debian-based Linux distribution):
    ---------------------------------------------------------
    
        sudo apt-get install libtre-dev libtre5

    On Mac OS X 
    -----------

    via macports [http://www.macports.org/] :

        sudo port install tre

    or via homebrew [http://brew.sh] :

        brew install tre

    or via compiling direct source code:

        wget http://laurikari.net/tre/tre-0.8.0.tar.gz
        tar -zxvf tre-0.8.0.tar.gz
        cd tre-0.8.0
        ./configure
        make
        sudo make install

    Other Alternative Operating Systems
    -----------------------------------
    
    For other installation alternatives please visit the following web site:

        http://laurikari.net/tre/download/

zlib
====

On Ubuntu (or any other Debian-based Linux distribution):

    sudo apt-get install zlib1g zlib1g-dev
    
On Mac OS X the zlib library comes pre-installed. 

Usage of the example trimmer, fqgrep-trim.pl, provided in the scripts subdirectory of this git repository, may require the installation of the 'Path::Class' perl module (found on CPAN) onto your system.

As the root user, please try the following terminal command for "Path::Class" installation:

 cpan Path::Class

INSTALLATION

The installation process currently consists of a very simple Makefile.

Just do the following:

git clone git://github.com/indraniel/fqgrep.git; cd fqgrep; make; # try 'make genome' if at the Genome Center at Washington University # or would like to create an executable with all the # relevant libraries statically compiled into it # # try 'make macports' if installing on Mac OS X and you installed the # TRE library via macports (http://www.macports.org/)

The 'fqgrep' executable should be in the working directory. Afterwards, you can move the executable to wherever you wish. Usually, this is the directory "/usr/local/bin" .

USAGE & DETAILS

For more information about fqgrep and its associated scripts, please visit the following documentation page:

https://github.com/indraniel/fqgrep/wiki

AUTHOR

Indraniel Das (indraniel at gmail dot com)

ACKNOWLEDGEMENTS

This software was developed at the Genome Center at Washington University, St. Louis, MO.

Thanks to the Genome Center's Technology Development Informatics Group (Jasreet Hundal, Jason Walker, and Todd Wylie) for insightful discussions and feedback.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

DOI INFO

https://zenodo.org/badge/latestdoi/20108/indraniel/fqgrep

Created: March 15, 2011