jvarkit

FastqSplitInterleaved

Last commit

Split interleaved Fastq files.

Usage

Usage: fastqsplitinterleaved [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit
    -a
      (fastq1 file or '-' for stdout). Ignore 1st read if omitted. Optional.
    -b
      (fastq2 file or '-' for stdout). Ignore 2nd read if omitted. Optional.

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew fastqsplitinterleaved

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/fastq/FastqSplitInterleaved.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite fastqsplitinterleaved ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

```bash $ curl -sk “https://raw.githubusercontent.com/bigdatagenomics/adam/fff8ae259e8f6958eefd8de9a3ec39d33392fb21/adam-core/src/test/resources/interleaved_fastq_sample1.fq” |\ java -jar dist/fastqsplitinterleaved.jar -a - | grep “^@”

@H06HDADXX130110:2:2116:3345:91806/1 @H06HDADXX130110:1:2103:11970:57672/1 @H06JUADXX130110:1:1108:6424:55322/1

$ curl -sk “https://raw.githubusercontent.com/bigdatagenomics/adam/fff8ae259e8f6958eefd8de9a3ec39d33392fb21/adam-core/src/test/resources/interleaved_fastq_sample1.fq” |\ java -jar dist/fastqsplitinterleaved.jar -b - | grep “^@” @H06HDADXX130110:2:2116:3345:91806/2 @H06HDADXX130110:1:2103:11970:57672/2 @H06JUADXX130110:1:1108:6424:55322/2

$ curl -sk “https://raw.githubusercontent.com/bigdatagenomics/adam/fff8ae259e8f6958eefd8de9a3ec39d33392fb21/adam-core/src/test/resources/interleaved_fastq_sample1.fq” |\ java -jar dist/fastqsplitinterleaved.jar -a x1.fq.gz -b x2.fq.gz