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/