Swift
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Application data |
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| Created by | Nava Whiteford |
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| Principal bioinformatics method(s) | Base-calling |
| Created at | Sanger Institute |
| Maintained? | Maybe |
| Programming language(s) | C++ |
| Licence | LGPL |
| Operating system(s) | Linux |
Summary: Primary Data Analysis for the Illumina Solexa Sequencing Platform.
"Error: no local variable "counter" was set." is not a number.
The instrument vendors already supply software for processing this data of course. However, when source code is even available, it is not open source. This makes the development of this software by the community impossible, it also raises scientific concerns as the algorithms used to process the primary data are not open to peer review.
In addition to this Swift also has a number of other design goals which make it attractive:
- A single binary that goes from images to basecalls (no intermediate files required, cuts down on IO)
- Parallelisable down to the tile level (so you can fire off 800+ runs on a cluster)
- Maintainable extendable C++ (change algorithms and parameters easily)
- Better algorithms.
- Fast!
Links
References
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