How to change id in fasta file

Question

[Diego]

Hi all,

I think I have a simple question for you. I need to change the id of my sequences in fasta because they are too long:

>CAEGAH010000001.1 genome assembly, contig: scaffold9796, whole genome shotgun sequence

How can I change/reduce all the ids in my fasta file to something simple:

 >CAEGAH010000001.1

Thanks all!!

[barslmn]

This is a routine question. Please utilize the available search functionality.

replace fasta headers with another name in a text file

Help for changing fasta seq ID

Renaming fasta headers according to a matching name list

Answer 1

[slw287r]

gzip -cd old.fa.gz | cut -d' ' -f1 | gzip > new.fa.gz

Answer 2

[Diego]

I ended up using the package seqkit:

cat myfile.fna | seqkit replace -p "\s.+" > newfile.fna