[Bioperl-l] Announcing Bio::SFF

[Peter Cock]

On Mon, Dec 19, 2011 at 3:03 PM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> I don't have any Ion Torrent data first hand, and the public
>> samples I've seen were FASTQ not SFF. But I know a few
>> people with Ion Torrent machines that might be able to help…
>
> I can you let you have some Ion Torrent SFF files if it helps
>
> adam

Hi Adam,

I've just had a quick look at a file from an IonTorrent 314 chip
that a colleague kindly sent me, and that SFF file had no index
(but only 50k reads so this isn't so important).

If you can send me (and Leon?) one of two original SFF files that
would be useful, even if just to confirm that Ion Torrent's SFF files
do indeed typically lack an index. If that is the case, I may need to
remove the warning message Biopython currently prints when
indexing these files: No SFF index, doing it the slow way

Off list is fine if you'd like to keep the data private, use dropbox
or something if you don't have an FTP server.

Thanks,

Peter