Convert paired end fastq file to fasta format

Question

[Abdul Rafay Khan]

Merge reads1 and read2 by using shuffleSequences_fastq.pl script:

perl shuffleSequences_fastq.pl Read1.fastq Read2.fastq ReadsMerge.fastq

Now how to convert paired end fastq file into fasta format correctly?

[shenwei356]

Answer from HengLi: A: Fastq Convert To Fasta

[Brian Bushnell]

As much as I dislike the absence of reformat.sh from the solutions, I agree that this is a good answer.