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Hiroki 09-17-2012 08:18 PM

Combine pairend reads into one file for SOPRA
Hi there,

Sorry for a pitifully newbie question:confused:.

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


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

Thank you very much.


themerlin 09-17-2012 09:42 PM

Try either included with Velvet or this:

Hiroki 09-18-2012 12:40 AM

Hi themerlin,

Thanx a lot.
I will try it.



maubp 09-18-2012 01:37 AM

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 09-26-2012 08:58 PM

Hi maubp,

Thanks a lot:)

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