Combine paired-end fastq files
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 :)
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3 answers
Use a program from BBMap suite.
reformat.sh in1=R1.fq.gz in2=R2.fq.gz out=interleaved.fq.gz
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
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That is called an
interleavedfastq, so googling that should bring up some ideas.Thank you so much. I used interleave-fastq, it worked a charm :)