From fastq files to fasta

Question

[ateh]

Hi, I am fairly new to bioinformatics. I have a set of fastq files. I will like to get them to a fasta format for genome annotation using prokka. I will appreciate any guidance on how to go about this. Thanks.

[GenoMax]

Using reformat.sh from BBMap suite

reformat.sh -Xmx2g in=file.fastq.gz out=file.fa fastawrap=NN 

fastawrap will wrap the lines after a number of bases you set if you have long reads. (optional if you have short reads)

[swbarnes2]

I'm not familiar with the application; is a simple conversion what OP needs? Not making a consensus?

[GenoMax]

Probably not but we work our way through.

We start with this, if it is a simple request:

have a set of fastq files. I will like to get them to a fasta format

but since the next sentence says

genome annotation using prokka

they probably need to end up with this --> Is there a way to convert a FASTQ file to FASTA file?

[cmdcolin]

99% of the requests for "fastq to fasta" should not do that literal conversion. instead, you should be performing a genome assembly of the FASTQ reads into a de-novo genome assembly (which creates a fasta format file) or align your FASTQ reads to a reference genome. GenoMax summarized it in his comment below also From fastq files to fasta

[ateh]

Thank you. While genome alignment tool will you recommend. I know there are a handful out there but will appreciate your thoughts.

Answer 1

[Andrzej Zielezinski]

You can use SeqKit to convert multiple FASTQ files into a single FASTA file.

seqkit fq2fa file1.fastq file2.fastq -o outfile.fasta

[ateh]

Thank you for your suggestion. With this output can I go ahead and do another analysis like snp calling, and annotations to gff?

[GenoMax]

No you can't. This is simply converting fastq format reads to fasta format reads. You are not getting a consensus fasta for your genome.