Hello,
I want to combine pair-end illumina fastq file and convert them into a single fasta file.
Welcome @clahey
You can use tools to concatenate sequences together and then convert the format but I’m wondering what your larger goal is. Are you concerned about redundancy? Do you want to assemble the reads? Do the reads represent RNA or DNA? Are these short reads?
We have tutorials here that may help you to get oriented.
Maybe try a search with keywords, or navigate by the different analysis domains?
This is one example where the initial fastq reads were assembled into in a consensus fasta format.
Hope this helps and you can ask follow up questions! 
These links/tutorials are very helpful. Thank you Jennifer
1 Like