Reverse complement fastq to fastq/a

When dealing with long insert mate pairs, some tools like Reapr might need the reads to be reverse complemented fastq in order to run the tool. So, I started searching for some softwares which can actually do what I wanted that.

One of the tool, I most of the times used was fastx_toolkit. It has a utility called fastx_reverse_complement by which I could convert all fastq to rc fastq files.

FASTQ to REV-COMP FASTQ:

$ fastx_reverse_complement -i sample.fastq -o rc_sample_fastx_tk.fastq

FASTQ to REV-COMP FASTA:

Sometimes, we might have to reverse complement fastq and need to convert to fasta file. This could be achieved by running revseq tool in EMBOSS with the following command:

$ revseq -sequence sample.fastq -outseq rc_sample.fasta -notag

* If there is a following error

fastx_reverse_complement: Invalid quality score value (char '0' ord 48 quality value -16) on line 4

Try pasting "-Q33" (without quotes) after fastx_reverse_complement.