Package org.biojava.nbio.sequencing.io.fastq

FASTQ and variants sequence format I/O.

To read from an Illumina variant FASTQ sequence file:

 FastqReader reader = new IlluminaFastqReader();
 for (Fastq fastq : reader.read(new File("illumina.fastq"))
 {
   // ...
 }
 

To write to an Sanger variant FASTQ sequence file:

 Collection<Fastq> fastq = ...;
 SangerFastqWriter writer = new SangerFastqWriter();
 writer.write(new File("sanger.fastq"), fastq);
 

For further documentation on the FASTQ sequence format, its variants, and how they are handled in O|B|F projects, see:

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
Nucleic Acids Research, doi:10.1093/nar/gkp1137