Therefore, using CTGTCTCTTATA for -x and -y should do the job. Other tools like Cutadapt also use this sequence as default for Nextera trimming.
Details about the Nextera transposase adapter sequences can be found here on page 12. The reverse complements of Read1 and Read2 are the sequences you get from the sequencing in case you sequence beyond your insert, which is then CTGTCTCTTATA for both reads, as mentioned above.
Hello, I am referring to the already closed Issue #16, where I think the provided -x/-y sequences are not correct: https://github.com/relipmoc/skewer/issues/16
The provided sequences do remove parts of the adapters but miss the Nextera Read Primer sequences, colored light blue and orange in the following picture: http://openwetware.org/images/0/07/Nextera_Illumina_fig1.gif
Therefore, using CTGTCTCTTATA for -x and -y should do the job. Other tools like Cutadapt also use this sequence as default for Nextera trimming. Details about the Nextera transposase adapter sequences can be found here on page 12. The reverse complements of Read1 and Read2 are the sequences you get from the sequencing in case you sequence beyond your insert, which is then CTGTCTCTTATA for both reads, as mentioned above.