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Fqutils provides a basic set of bioinformatics tools for working with sequence data in FASTQ format. It complements Greg Hannon's excellent Fastx Toolkit suite. One characteristic of Fqutils is that it correctly handles the full FASTQ format as described by

Peter J. A. Cock, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, Peter M. Rice. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research (2010) 38 (6): 1767-177,

which specifically allows for multiline sequence and quality score information per record. Fqutils is intended to be useful as part of the early portions of postsequencing pipelines and quality assessment processes. See http://crowja.github.com/fqutils for more details.