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Reports
I'm creating this area for techreports and other useful documentation, please feel free to add your own. If you have any questions about my reports or would like to develop them further please contact me at: nw3 at sanger dot ac dot uk or new at sgenomics dot org - Nav
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An Investigation in to early cycle errors in a single run
- The Solexa technology shouldn't produce early cycle errors. In the document we investigate the sources of early cycle errors in a single run on a GA1 instrument at the Sanger Institute.
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The Solexa Pipeline
- This document describes the Solexa pipeline. It is mostly the result of digging around in the source code and attempting to describe the algorithms. Currently this document is focused on image analysis.
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Quality scores conversion chart
- Quick chart for converting between Phred/Solexa and probability.
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The Information Content of ABI SOLiD 2 Base Encoded Reads
- The title isn't really appropriate, this document gives a brief summary of the ABI SOLiD tech and then runs the numbers a little. It might be interesting to develop some of these ideas in to a paper at some point. Perhaps adding an analysis of the Yoruba dataset at some point.
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Color space
- Because in color space no-one can hear you scream ?
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Benchmarking Assembly Algorithms
- This is a paper I was working on where traditional assemblers were benchmarked for short read data, it never made it to publication though one day it would be nice to finish it off. Comments are welcome.
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Next-gen sequencing Primer
- A shortish primer on next-gen sequencing mostly focusing on primary data analysis and error rates.
1000 Genomes
