Probabilistic base calling of Solexa sequencing data

doi:10.1186/1471-2105-9-431

BMC Bioinformatics

Volume 9

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Rougemont J
Amzallag A
Iseli C
Farinelli L
Xenarios I
Naef F

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Farinelli L
Xenarios I
Naef F
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Methodology article

Probabilistic base calling of Solexa sequencing data

Jacques Rougemont¹^,3 , Arnaud Amzallag¹^,3 , Christian Iseli²^,3 , Laurent Farinelli⁵ , Ioannis Xenarios³^,4 and Felix Naef¹^,3

¹School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland

²Ludwig Institute for Cancer Research (LICR), Bâtiment Génopode, Université de Lausanne, 1015 Lausanne, Switzerland

³Swiss Institute of Bioinformatics (SIB), Bâtiment Génopode, Université de Lausanne, 1015 Lausanne, Switzerland

⁴Vital-IT, Bâtiment Génopode, Université de Lausanne, 1015 Lausanne, Switzerland

⁵Fasteris SA, P.O. box 28, 1228 Plan-les-Ouates, Switzerland

author email corresponding author email

BMC Bioinformatics 2008, 9:431doi:10.1186/1471-2105-9-431


Published:	13 October 2008

Additional files

Additional File 1:

Signal over noise decays with sequencing cycle number. Histograms of the raw fluorescence intensities are shown for cycles 5, 15, 25, and 35. The separation between signal and noise is increasingly blurred and faster in the A and G channels than in the C and T channels. Red lines indicate a fit by a mixture of two Gaussians distributions with blue vertical bars indicating the mean and one standard deviation for the highest component of the mixture.

Format: PNG Size: 17KB Download file

Additional File 2:

Correction of positional bias. A. Images show local averages of the fluorescence intensities across the area of a tile. The center of the tile is clearly brighter than the edges. B. After correction by lowess fit, the averages are visually more constant across the tile.

Format: PNG Size: 20KB Download file

Additional File 3:

Increased coverage of Rolexa data relative to Solexa data on a human sample. A complete sequencing lane (330 tiles) was analyzed with Rolexa and Solexa pipelines. The X axis represents the number of nucleotides covered by the sequences of a tile with Rolexa base-calling and the Y axis represents the ratio with the corresponding Solexa base-calling with tags restricted to 25 bases or the full 36 bases length.

Format: PNG Size: 15KB Download file