5 - Fastq to fasta conversion.

This perl one-liner will convert a fastq file into a fasta file. The following script was written by Robert Schmieder in the Edwards Bioinformatics Lab at San Diego State University.

Here is the link to the original webpage:

http://edwards.sdsu.edu/labsite/index.php/robert/289-how-to-convert-fastq-to-fasta

Here is the one-line command:

cat file.fastq | perl -e '$i=0; while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3)$i++;}' > file.fasta