[EMBOSS] fasta single-line sequence format?

Peter Cock p.j.a.cock at googlemail.com
Tue Aug 27 14:51:03 UTC 2013

On Tue, Aug 27, 2013 at 3:08 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Is there a name for the FASTQ analog?  Maybe 'unwrapped'? :)

No, EMBOSS always write unwrapped FASTQ on output,
but accepts line wrapped FASTQ on input.

> Neils: Re: 'Most genome packages use it': can you specify?
> Most genome packages I know allow the flexibility to use
> standard line-wrapped FASTA as well, so coding an indexing
> scheme for a non-standard FASTA alone seems… tricky.
> Unless you intend on allowing both, and 'unwrapped' is just
> for optimization.
> chris f.

e.g. faidx by Heng Li allows line wrapped FASTA, with the
proviso that each record uses the same line wrapping length
(so it can't cope with arbitrary FASTA files).


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