| Name | Description | Type | Package | Framework |
| Fastq | FASTQ formatted sequence. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| FastqBuilder | Fluent builder API for creating FASTQ formatted sequences. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| FastqReader | Reader for FASTQ formatted sequences. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
| FastqTools | Utility methods for FASTQ formatted sequences. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| FastqVariant | FASTQ sequence format variant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| FastqWriter | Writer for FASTQ formatted sequences. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
| IlluminaFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| IlluminaFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| ParseListener | Low-level event based parser callback. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SangerFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SangerFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SolexaFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SolexaFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| StreamListener | Event based parser callback. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |