Do I have to add /1 & /2 to the forward and reverse reads for PE data

[Salim B]

Hi Abyssers,

I have a basic question about the fastq format required for abyss to run a PE assembly.

I run QC using Trimmomatic which generates two R1 & R2 files but the read names do no have a /1 & /2 suffix. Do I have to add /1 & /2 to every read or should using pe="r1.fastq r2.fastq" suffice?

What if I run abyss-tofastq --interleave --fastq r1.fastq r2.fastq > r12.fastq work?

Regards,

/SB

[Ben Vandervalk]

Hi Salim,

pe="r1.fastq r2.fastq" should suffice.

ABySS requires that either:

(i) the read names for both reads are identical, OR

(ii) the read names have an identical prefix, followed by "/1" and "/2", respectively.

- Ben

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