jvarkit

FastqRevComp

produces a reverse-complement fastq (for mate pair alignment see http://seqanswers.com/forums/showthread.php?t=5085 )

Usage

Usage: fastqrevcomp [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
    -1
       interleaced input : only reverse complement R1
      Default: false
    -2
       interleaced input : only reverse complement R2
      Default: false

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 fastqrevcomp

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/FastqRevComp.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 fastqrevcomp ? 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

without revcomp

$ gunzip -c mate.fastq.gz | head -n 8

@M00785:3:000000000-A60G6:1:1101:15339:1356 1:N:0:1
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTCTTTCTTTTCTTTTTTTTTTTTTTCTTTTTTTTTTTTTTCTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTTTCTTTCTTTCTTTTTTTTTTCTCTCTCTTTTTTTTTCTTTCTTTTTTTCCTTTTTCCTTTTTCTTTCTTCTTTTTTCTTCTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
+
111>>>11>000//A//A>>>/>/>><//<<<//<-<@--/00000-/00:0::000000:9---------//9///--9------//9/99-9----9//////-----9-----9--///9/99-;/99//////99/;/-99--/////////9;9---9//9///;;//-9////////////9///://99//9///-//9/999//99-/9/;:/9--;---9-9---@--------;---//9/
@M00785:3:000000000-A60G6:1:1101:15206:1568 1:N:0:1
GCTGGTGTTCCTCAGCCACGGGGGTAGGGAACAGGCGTTACCACTTACATTCCCAGGACACCATGGCCTGTCTCTTATACACATCTAGATGTGTATAAGAGACAGGGTAACTACAATGGACCCCTTGCAGCCTGGAAGGGCCAGCAGTTCACTTTTCCAAGAGCAGCCGTGCATTCTGCACCTGAGTGTTGGCCTCTCCTGGCCATAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATC
+
11>11BFAA@@DFB1BB1FECE?CE//AC0CFHFGFCGGGGF1BFHGHFHHHFHFHGEFBGFHFBCFGHGHFGEFGBGFGFHFHHHFE2F2F1FFHFFFHGEGB0AEHHEHHHFFFGBFFGHGGGHHFFHFFG0/0CHGGGGGHGHHHGHGHHHHHHHHHHGHGHGHHGGCGHHHHHHHHHHHHHHGHHHAEHGGGGGGGGFGGGGFGFFGGGGBBEGEGGGFFF?FEFFFFFFFFFFFFFFFF?@FFFFB

with revcomp

 gunzip -c mate.fastq.gz | head -n 8 | java -jar dist/fastqrevcomp.jar

@M00785:3:000000000-A60G6:1:1101:15339:1356 1:N:0:1
AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAGAAAAAAGAAGAAAGAAAAAGGAAAAAGGAAAAAAAGAAAGAAAAAAAAAGAGAGAGAAAAAAAAAAGAAAGAAAGAAAAAAAAGAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAGAAAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
/9//---;--------@---9-9---;--9/:;/9/-99//999/9//-///9//99//:///9////////////9-//;;///9//9---9;9/////////--99-/;/99//////99/;-99/9///--9-----9-----//////9----9-99/9//------9--///9//---------9:000000::0:00/-00000/--@<-<//<<<//<>>/>/>>>A//A//000>11>>>111
@M00785:3:000000000-A60G6:1:1101:15206:1568 1:N:0:1
GATACATCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTATGGCCAGGAGAGGCCAACACTCAGGTGCAGAATGCACGGCTGCTCTTGGAAAAGTGAACTGCTGGCCCTTCCAGGCTGCAAGGGGTCCATTGTAGTTACCCTGTCTCTTATACACATCTAGATGTGTATAAGAGACAGGCCATGGTGTCCTGGGAATGTAAGTGGTAACGCCTGTTCCCTACCCCCGTGGCTGAGGAACACCAGC
+
BFFFF@?FFFFFFFFFFFFFFFFEF?FFFGGGEGEBBGGGGFFGFGGGGFGGGGGGGGHEAHHHGHHHHHHHHHHHHHHGCGGHHGHGHGHHHHHHHHHHGHGHHHGHGGGGGHC0/0GFFHFFHHGGGHGFFBGFFFHHHEHHEA0BGEGHFFFHFF1F2F2EFHHHFHFGFGBGFEGFHGHGFCBFHFGBFEGHFHFHHHFHGHFB1FGGGGCFGFHFC0CA//EC?ECEF1BB1BFD@@AAFB11>11

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