From fastq files to fasta
1
0
Entering edit mode
9 weeks ago
ateh • 0

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.

genome annotation fasta Fastq • 445 views
ADD COMMENT
0
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
9 weeks ago

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

seqkit fq2fa file1.fastq file2.fastq -o outfile.fasta
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 868 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6