Jun's Blog

Output, activities, memo and etc.

Converting FASTQ format to FASTA format

The FASTQ format is to combine the FASTA format + Quality info. Therefore, we can convert the FASTQ format into FASTA format, removing only the quality info.

Here is the way: https://bioinformaticsworkbook.org/dataWrangling/fastaq-manipulations/converting-fastq-format-to-fasta.html#gsc.tab=0

I think the easiest way is to use the sed command in the list of the ways.

$ sed -n '1~4s/^@/>/p;2~4p' INFILE.fastq > OUTFILE.fasta

-n: quiet option. Suppress automatic printing of pattern space.

Hmm, it's difficult to understand what the expression argument of the sed is doing.

References