Combine pairend reads into one file for SOPRA

[Hiroki]

Hi there,

Sorry for a pitifully newbie question.

How can I combine two fasta files, read 1 and read2 from a Illumina pairend run into a single file as this:

>seq1read1
cagtgtcgaggaac...
>seq1read2
gatatagagatctac...
>seq2read1
cagtgtcgaggttt...
>seq2read2
gatatagagatcgta...

I want to try SOPRA and it requires the format above as matepair read input.

Thank you very much.

Hiroki

[themerlin]

Try either shuffleSequences_fastq.pl included with Velvet or this:

http://www.ngcrawford.com/2012/03/28/interleave-paired-end-reads/

[Hiroki]

Hi themerlin,

Thanx a lot.
I will try it.

Best,

Hiroki

[maubp]

If you want more options, try searching for interleaving, the resulting file is often called an interleaved FASTA (likewise with FASTQ), because you interleave the forward and reverse read files to combine them.

[Hiroki]

Hi maubp,

Thanks a lot