jvarkit

FastqSplit

Split Fastq files into multiple files.

Usage

Usage: fastqsplit [options] Files
  Options:
    -async, --async
      use async I/O
      Default: false
    -n, -N, --count
      number of reads per file. will be generated. Or use option 's'.
      Default: -1
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -ii, --input-interleaved
      input is paired interleaved
      Default: false
    -m, --manifest
      Optional manifest file
    -md5, --md5
      write md5 file
      Default: false
  * -o, --output
      Output file name. It MUST  end with a fastq suffix and MUST contain the 
      word __TOKEN__
    -oi, --output-interleaved
      output is interleaved
      Default: false
    -s, -S, --splits
      number of splits. At most 'x' (pair-of)files will be generated. Or use 
      option 'n'
      Default: -1
    -validate, --validate
      validate read names
      Default: false
    --version
      print version and exit

Keywords

• fastq

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

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

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

Creation Date

20200327

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/fastq/FastqSplitTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite fastqsplit ? 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

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