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Generate statistics on and validate fastq files
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sanger-pathogens/fastqcheck
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fastqcheck is a program that reads fastq files (sequencing data: http://maq.sourceforge.net/fastq.shtml). It generates statistics about the files (for example, how many reads and bases there were). It can be used as a validator of fastq files (though is perhaps stricter that the spec). Usage: $ fastqcheck lane1.fastq > lane1.fastq.fastqcheck $ gunzip -c lane1.fastq.gz | fastqcheck > lane1.fastq.gz.fastqcheck Or using Docker: $ docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/fastqcheck fastqcheck lane1.fastq > lane1.fastq.fastqcheck The software is built and installed in the standard manner using configure and make. Installation instructions are in the INSTALL file. [![Build Status](https://travis-ci.org/sanger-pathogens/fastqcheck.svg?branch=master)](https://travis-ci.org/sanger-pathogens/fastqcheck) COPYRIGHT & LICENSE ------------------- Copyright (c) 1993, 2006, 2009, 2010, 2013 Genome Research Limited. This file is part of fastqcheck. fastqcheck 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. If not, see L<http://www.gnu.org/licenses/>. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads 'Copyright (c) 2005, 2007- 2009, 2011-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012' and a copyright statement that reads "Copyright (c) 2005-2012' should be interpreted as being identical to a statement that reads 'Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012'."
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Generate statistics on and validate fastq files
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