Combine paired-end fastq files

Question

[112498262]

I am trying to use SCARPA for scaffolding. I have been given two separate paired-end fastq files, one containing each forward read and the second containing the corresponding reverse reads. SCARPA requires the read data to be in a single fastq format, whereby the forward and reverse read of each pair are consecutive in the file.

How do I merge my two fastq files to one file in the required format?

Thanks :)

[WouterDeCoster]

That is called an interleaved fastq, so googling that should bring up some ideas.

[112498262]

Thank you so much. I used interleave-fastq, it worked a charm :)

Answer 1

[GenoMax]

Use a program from BBMap suite.

reformat.sh in1=R1.fq.gz in2=R2.fq.gz out=interleaved.fq.gz

Answer 2

[ChillarAnand]

We can use seqfu tool to interleave them.

Install anaconda and then run

$ conda install -c conda-forge -c bioconda "seqfu>1.0"

To interleave them, run

$ seqfu interleave -1 SRR_1.fastq.gz -2 SRR_2.fastq.gz > SRR.fastq

Answer 3

[xiaoguang]

you can use this software Flash2