jvarkit

FastqGrep

Last commit

Grep reads names in fastq

DEPRECATED

use picard

Usage

Usage: fastqgrep [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -R
      add the read
      Default: []
    -V
      invert)
      Default: false
    -f
       file containing a list of read names
    -n
      when found, remove the read from the list of names when found more that 
      'n' time (increase speed)
      Default: -1

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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/misc/FastqGrep.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite fastqgrep ? 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