.nt assemblage file, can I convert to FASTA?

Question

[YOUSEUFS]

Hi all

I've been given a .nt (never come across these before) file of a bacterial genome which I want to index to use with bowtie but bowtie accepts .fasta and not .nt. Could you guys explain what the hell a .nt file is and can I convert it to .fasta?

Huge thanks in advance!

[Brian Bushnell]

Have you tried looking at the contents of the file? It is probably an incorrectly named fasta file.

[YOUSEUFS]

The first few lines look like this (it might not show correctly here)

....|....| ....|....| ....|....| ....|....| ....|....| ....|....|

 5          15         25         35         45         55    
scaffold00   ttggttaggt aaggaagtag tattgctact actccctccc ttagaaacgc agcatgcagg

scaffold00   ttctgctata tatctatttc cgtgagaatc cttgcagaga acatcaacaa tactttgttt

scaffold00   caacttaatt agaagtttag ctttaacttt aaatggacta ctcaaccgtg acagacttag

[Brian Bushnell]

That looks like Phylip, which is a really irritating format to deal with. I'd just ask the person for a fasta file instead, or download one yourself if you know the exact bacterial strain.