How to convert FASTQ to FASTA

Question

[Ching]

I downloaded a fastq.gz file from ENA browser but can't open it. How can I convert the file to fasta format? https://www.ebi.ac.uk/ena/browser/view/SRR16952091?show=reads

[cpad0112]

> but can't open it

Can you elaborate on this?

Answer 1

[GenoMax]

Assuming you have done nothing else to the file you can use reformat.sh from BBMap suite.

reformat.sh -Xmx2g in=SRR16952091.fastq.gz out=SRR16952091.fasta

Output file will be in fasta format but uncompressed. So it will be significantly larger. To keep it compressed you can add .gz extension to fasta file name.

Answer 2

[jkim]

seqtk. https://github.com/lh3/seqtk

seqtk seq -a in.fq.gz > out.fa

Answer 3

[margarett]

You can also use Galaxy to convert your files [https://usegalaxy.org/]