Sff2fastq
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Application data |
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| Created by | Indraniel Das |
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| Principal bioinformatics method(s) | conversion |
| Technology | 454 |
| Created at | The Genome Center at Washington University, St. Louis, MO. |
| Maintained? | Yes |
| Input format(s) | SFF |
| Output format(s) | FASTQ |
| Operating system(s) | Linux |
| Contact: | indraniel@gmail.com |
Summary: The program 'sff2fastq' extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.
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Description
In the world of 454 sequencing, Roche 454 has their own set of tools to work with the data. Unfortunately, they are not freely available. While the 454 tools from Roche provide a way to convert their data into a FASTA file format, another device independent sequence file format; there is not a direct SFF to FASTQ conversion utility.
To that end, and for curiosities sake, I decided to write a program to do so, called sff2fastq. The idea is by no means unique. There are other similar tools such as flower (haskell-based) and sff_extract (python-based), and other alternative approaches as discussed on seqanswers. As they say, variety is the spice of life.
Links
References
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