Question

Fasta/Fastq File Conversion To Sff File

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12.5 years ago

Ram ▴ 20

Hi

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

Cheers Ram

fasta fastq conversion format • 7.5k views

ADD COMMENT • link updated 10.1 years ago by Biostar 20 • written 12.5 years ago by Ram ▴ 20

score 4 · Answer 1 · 2011-11-23

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12.5 years ago

Damian Kao 16k

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 COMMENT • link 12.5 years ago by Damian Kao 16k

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

ADD REPLY • link 12.5 years ago by Ram ▴ 20

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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 REPLY • link 12.5 years ago by Damian Kao 16k

score 1 · Answer 2 · 2011-11-23

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12.5 years ago

Martin A Hansen 3.0k

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 COMMENT • link 12.5 years ago by Martin A Hansen 3.0k

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

ADD REPLY • link 12.5 years ago by Ram ▴ 20