Question: Fasta/Fastq File Conversion To Sff File
2
gravatar for Ram
2.4 years ago by
Ram20
Ram20 wrote:

Hi

Can anyone help to find the script or tool to convert fasta/fastq file to sff format? Thanks for the help..

Cheers Ram

ADD COMMENTlink modified 9 days ago by Biostar ♦♦ 0 • written 2.4 years ago by Ram20
4
gravatar for Damian Kao
2.4 years ago by
Damian Kao10k
UK
Damian Kao10k wrote:

There isn't enough information contained in a fasta file for converting to SFF. SFFs are flowgram files that contain information on sequence, quality and signal strengths. Why do you want to convert fasta to SFF? Newbler and Mira will both take in fasta files if that's what you want to use it for.

You can find information on SFF files here: http://contig.wordpress.com/2010/10/28/newbler-input-i-the-sff-file/

It is also a great blog for everything you want to know about how Newbler works.

ADD COMMENTlink written 2.4 years ago by Damian Kao10k

hi Actually working on AVA and I know it only takes sff files but I have only fasta file.

ADD REPLYlink written 2.4 years ago by Ram20

You might have to just bite the bullet and align your reads and call snps with other software. It won't be as straight forward as using the amplicon variant analyzer, but at least you know exactly what is going on with the analysis.

ADD REPLYlink written 2.4 years ago by Damian Kao10k
1
gravatar for Martin A Hansen
2.4 years ago by
Martin A Hansen2.7k
Denmark
Martin A Hansen2.7k wrote:

This can't be done. SFF contains more information, namely flow gram data, than fasta/fastq can encode. You can use sfffile to obtain a subselection of a SFF file. See the documentation.

ADD COMMENTlink written 2.4 years ago by Martin A Hansen2.7k

Hi Thanks a lot. That helped me to understand the difference between sff files and fasta/fastq files.

ADD REPLYlink written 2.4 years ago by Ram20
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