Package org.biojava3.sequencing.io.fastq

FASTQ and variants sequence format I/O.

See:
          Description

Interface Summary
FastqReader Reader for FASTQ formatted sequences.
FastqWriter Writer for FASTQ formatted sequences.
ParseListener Low-level event based parser callback.
StreamListener Event based parser callback.
 

Class Summary
Fastq FASTQ formatted sequence.
FastqBuilder Fluent builder API for creating FASTQ formatted sequences.
FastqTools Utility methods for FASTQ formatted sequences.
IlluminaFastqReader Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
SangerFastqReader Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SolexaFastqReader Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.
 

Enum Summary
FastqVariant FASTQ sequence format variant.
 

Package org.biojava3.sequencing.io.fastq Description

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

Since:
3.0.3