CODEWITHSUNDEEP
bioinformaticsfastagenomesequencing
Litsa Abdelnour
Litsa Abdelnour

Reputation: 1

How can I convert a fsa_nt file to FASTA?

Im trying to convert a file downloaded from NCBI containing contigs of a bacterial genome. For further analysis I need to have it in FASta format.

I tried converting via seqkit, but it does not work.

Upvotes: 0

Views: 740

Answers (1)

tla
tla

Reputation: 1004

.fsa_nt extension means that the file is already in the FASTA format. NCBI GenBank release notes describe .fsa_nt files as "Nucleotide FASTA".

Typical files downloaded from NCBI have .fsa_nt.gz extension. These files are already in FASTA format, compressed in gzip. You can decompress them with gunzip or zcat.

For example, in *nix system you can do this to download and decompress an .fsa_nt.gz file:

curl ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/LN/TK/LNTK01/LNTK01.1.fsa_nt.gz | gunzip > LNTK01.1.fasta

Upvotes: 1

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