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title BioJava:CookBook3:FASTQ
permalink wiki/BioJava%3ACookBook3%3AFASTQ

How do I work with nextgen sequencing reads in FASTQ format?

The org.biojava3.sequencing.io.fastq package provides support for reading and writing nextgen sequencing reads in FASTQ format (FastqReader and FastqWriter, respectively) and for converting FASTQ sequences into proper biojava3 DNASequences for analysis purposes (FastqTools).

The following code snippets demonstrate how to use the APIs for common use cases.

Convert between FASTQ variants

fastqWriter = new SangerFastqWriter(); fastqWriter.write(new
File("sanger.fastq"), fastqReader.read(new File("illumina.fastq")));

Convert only long sequences

fastqWriter = new SangerFastqWriter(); FileWriter fileWriter = new
FileWriter(new File("sanger.fastq"))));

for (Fastq fastq : fastqReader.read(new File("illumina.fastq"))) {

` if (fastq.getSequence().length() > 16)`  
` {`  
`   fastqWriter.append(fileWriter, fastq);`  
` }`

} ```

### Convert between FASTQ variants using streaming API

```java FastqReader fastqReader = new IlluminaFastqReader();
InputSupplier inputSupplier = Files.newReaderSupplier(new
File("illumina.fastq")); final FastqWriter fastqWriter = new
SangerFastqWriter(); final FileWriter fileWriter = new FileWriter(new
File("sanger.fastq"))));

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     fastqWriter.append(fileWriter, fastq);`  
`   }`  
` });`

Convert only long sequences using streaming API

InputSupplier inputSupplier = Files.newReaderSupplier(new
File("illumina.fastq")); FastqWriter fastqWriter = new
SangerFastqWriter(); FileWriter fileWriter = new FileWriter(new
File("sanger.fastq"))));

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     if (fastq.getSequence().length() > 16)`  
`     {`  
`       fastqWriter.append(fileWriter, fastq);`  
`     }`  
`   }`  
` });`

Count sequences

int count = 0; for (Fastq fastq : fastqReader.read(new
File("illumina.fastq"))) {

` count++:`

} System.out.println(count); ```

### Count sequences using streaming API

```java FastqReader fastqReader = new IlluminaFastqReader();
InputSupplier inputSupplier = Files.newReaderSupplier(new
File("illumina.fastq"));

final AtomicInteger count = new AtomicInteger();
fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     count.incrementAndGet();`  
`   }`  
` });`

System.out.println(count.get()); ```

### Count sequences using low-level API

```java FastqReader fastqReader = new IlluminaFastqReader();
InputSupplier inputSupplier = Files.newReaderSupplier(new
File("illumina.fastq"));

final AtomicInteger count = new AtomicInteger();
fastqReader.parse(inputSupplier, new ParseAdapter()

` {`  
`   @Override`  
`   public void complete() throws IOException`  
`   {`  
`     count.incrementAndGet();`  
`   }`  
` });`

System.out.println(count.get()); ```

### Pattern match description lines using low-level API

```java final Pattern pattern = Pattern.compile("^HWUSI-EAS100R:.\*$");
FastqReader fastqReader = new IlluminaFastqReader(); InputSupplier
inputSupplier = Files.newReaderSupplier(new File("illumina.fastq"));

fastqReader.parse(inputSupplier, new ParseAdapter()

` {`  
`   @Override`  
`   public void description(final String description) throws IOException`  
`   {`  
`     if (pattern.matches(description))`  
`     {`  
`       System.out.println(description);`  
`     }`  
`   }`  
` });`

Create DNASequences from FASTQ sequences

List<DNASequence> sequences = new LinkedList<DNASequence>();

for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {

` sequences.add(FastqTools.createDNASequence(fastq));`

} ```

### Create DNASequences with quality scores in QualityFeature from FASTQ sequences

```java FastqReader fastqReader = new SangerFastqReader();
List<DNASequence> sequences = new LinkedList<DNASequence>();

for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {

` sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));`

} ```

### Create DNASequences with quality scores in QualityFeature and error probabilities in QuantityFeature from FASTQ sequences

```java FastqReader fastqReader = new SangerFastqReader();
List<DNASequence> sequences = new LinkedList<DNASequence>();

for (Fastq fastq : fastqReader.read(new File("sanger.fastq"))) {

` sequences.add(FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(fastq));`

} ```

### Create DNASequences with streaming API

```java FastqReader fastqReader = new SangerFastqReader(); InputSupplier
inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
List<DNASequence> sequences = new LinkedList<DNASequence>();

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     sequences.add(FastqTools.createDNASequence(fastq));`  
`   }`  
` });`

Create DNASequences with quality scores in QualityFeature from FASTQ sequences with streaming API

inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
List<DNASequence> sequences = new LinkedList<DNASequence>();

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));`  
`   }`  
` });`

Create DNASequences with quality scores in QualityFeature and error probabilities in QuantityFeature from FASTQ sequences with streaming API

inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
List<DNASequence> sequences = new LinkedList<DNASequence>();

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     sequences.add(FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(fastq));`  
`   }`  
` });`

Calculate mean p scores using streaming API

inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
SummaryStatistics stats = new SummaryStatistics(); StringBuilder sb =
new StringBuilder(512);

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     stats.clear();`  
`     for (Double errorProbability : FastqTools.errorProbabilities(fastq))`  
`     {`  
`       stats.addValue(errorProbability);`  
`     }`  
`     sb.delete(0, sb.length());`  
`     sb.append(fastq.getDescription());`  
`     sb.append("\t");`  
`     sb.append(stats.getMean());`  
`     sb.append("\t");`  
`     sb.append(stats.getStandardDeviation());`  
`     System.out.println(sb.toString());`  
`   }`  
` });`

Calculate mean p scores using streaming API and double array

inputSupplier = Files.newReaderSupplier(new File("sanger.fastq"));
SummaryStatistics stats = new SummaryStatistics(); StringBuilder sb =
new StringBuilder(512);

fastqReader.stream(inputSupplier, new StreamListener()

` {`  
`   @Override`  
`   public void fastq(final Fastq fastq)`  
`   {`  
`     stats.clear();`  
`     int size = fastq.getSequence().length();`  
`     double[] errorProbabilities = FastqTools.errorProbabilties(fastq, new double[size]);`  
`     for (int i = 0; i < size; i++)`  
`     {`  
`       stats.addValue(errorProbabilities[i]);`  
`     }`  
`     sb.delete(0, sb.length());`  
`     sb.append(fastq.getDescription());`  
`     sb.append("\t");`  
`     sb.append(stats.getMean());`  
`     sb.append("\t");`  
`     sb.append(stats.getStandardDeviation());`  
`     System.out.println(sb.toString());`  
`   }`  
` });`