fasta+qual = sff??

[vincebrown]

Dear Bioinformatists,

The data I have received has 454 pyrosequence reads in Fasta format and respective quality scores as a .qual file.

I am using Newbler to perform the assembly. Just wanted to know if I could use these two files to create a sff file as Newbler's efficiency lies in inputting this file.

Thank You!

[kmcarr]

While there are a number of tools for going from SFF --> Fasta+Qual I know of no tools to go the other direction. SFF is a binary file format which stores, in addition to the sequence and q-score values, the flow values for the run as well. This information has been lost in the conversion to Fasta+Qual.

Contact the original sequence provider to see if you can obtain the SFF files.

[vincebrown]

Thanks a lot.

I was about to request my sequence provider of the same as well.
Even I could not find a tool that could do the reverse conversion.

Vince

[maubp]

You can't do FASTA+QUAL to SFF, or FASTQ to SFF. These simple text files lack the flow space information.

[motan]

Even I could not find a tool that could do the reverse conversion. Vince

Just use the SFF Workbench to see a graphic representation of your SFF file. You will see there is a lot of info in a SFF file. On the other hand, a FASTA file contains nothing else that bases. Once you convert it from a SFF to a simple format (such as FASTA) the information lost is irreversible.

And it is not all about the reads. The SFF contains additional info such as the Roche manifest or the clipping info.


(sorry, I couldn't find a smaller screenshot)