tools for sequence separation

Question

[mheyda]

Does anyone know any tool which would be exactly opposite of Shuffle Sequencing (SS). As you might know, SS is used to merge reads of two paired end reads fastq file into one single file fastq file. I know it is easy to write a script to separate these reads into initial files, but I want to use some standard tools if exists.

[iraun]

Do you mean that you have paired end reads merged in a one file and you would like to separate them into two separated files?

[mheyda]

yes exactly

[iraun]

Maybe you can try the solutions proposed here Fastq Splitter For Paired End Reads?

[mheyda]

My question is a little bit different, SS don't merge lines of two files into one line, it only writes the line of two files in sequential order one by one (one block from the left file and another block from the right file), but it keeps the initial order.

[george.ry]

So it's just an interleaved FASTQ? deinterleave fastq file