We often have people ask us how to convert fastq files to fasta format. We have a variety of code on this website, but sometimes that is not easy enough.

Here are a couple of ways to do it on the command line: using a PERL script written by Bas, using the command line, or using prinseq-lite. Here is a C++ version that you can compile (e.g. with c++ -o fastq2fasta fastq2fasta.cpp) and run on your machine.

We also have a simple form that converts fastq files to fasta files (DNA only … it does not give you the quality scores).