fastx_toolkit
zcat -f '$input' | fastx_reverse_complement -v -o $output
**What it does**
This tool reverse-complements each sequence in a library.
If the library is a FASTQ, the quality-scores are also reversed.
--------
**Example**
Input FASTQ file::
@CSHL_1_FC42AGWWWXX:8:1:3:740
TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
+CSHL_1_FC42AGWWWXX:8:1:3:740
33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
Output FASTQ file::
@CSHL_1_FC42AGWWWXX:8:1:3:740
TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
+CSHL_1_FC42AGWWWXX:8:1:3:740
26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
------
This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
.. __: http://hannonlab.cshl.edu/fastx_toolkit/