Base Caller Summaries - Revision history

Srashkin: /* References */

2010-03-12T21:04:23Z

References

← Older revision		Revision as of 17:04, 12 March 2010
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	Kao, W.-C., Stevens, K., Song, Y.S. (2009) BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing. ''Genome Research'' '''19''':1884-1895		Kao, W.-C., Stevens, K., Song, Y.S. (2009) BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing. ''Genome Research'' '''19''':1884-1895

			Kircher, M., Stenzel, U., Kelso, J. (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. ''Genome Biol.'' '''10(8)''':Article R83

	Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xenarios, I., Naef, F. (2008) Probabilistic base calling of Solexa sequencing data. ''BMC Bioinformatics'' '''9''':Article 431		Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xenarios, I., Naef, F. (2008) Probabilistic base calling of Solexa sequencing data. ''BMC Bioinformatics'' '''9''':Article 431

	Whiteford, N., Skelly, T., Curtis, C., Ritchie, M.E., Löhr, A., Zaranek, A.W., Abnizova, I., Brown, C. (2009) Swift: Primary data analysis for the Illumina Solexa sequencing platform. ''Bioinformatics'' '''25''':2194-2199		Whiteford, N., Skelly, T., Curtis, C., Ritchie, M.E., Löhr, A., Zaranek, A.W., Abnizova, I., Brown, C. (2009) Swift: Primary data analysis for the Illumina Solexa sequencing platform. ''Bioinformatics'' '''25''':2194-2199

Srashkin: /* Comparison */

2010-03-12T20:57:06Z

Comparison

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	*Unlike AltaCyclic, includes base-specific phasing parameters so can correct raw intensities for T accumulation		*Unlike AltaCyclic, includes base-specific phasing parameters so can correct raw intensities for T accumulation
	*Does not call an 'N' character for poor quality bases		*Does not call an 'N' character for poor quality bases
			*Process unique as causes of sequencing error not modeled separately
			**Consider causes together by using neighboring signals in statistical learning procedure

	==References==		==References==

Srashkin: /* Ibis */

2010-03-12T20:55:40Z

Ibis

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	==Ibis==		==Ibis==

			===Method===
	*Estimate sequencing chemistry model as a parameter directly from data using statistical learning		*Estimate sequencing chemistry model as a parameter directly from data using statistical learning
	*Training set from Bustard output using raw cluster intensities		*Training set from Bustard output using raw cluster intensities
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	**Half of this set used as a training set and the other half as a test set used to check results of training		**Half of this set used as a training set and the other half as a test set used to check results of training
	*Estimate parameters for calculating a quality score given class assignment and distances to the classification/decision boundary from SVM		*Estimate parameters for calculating a quality score given class assignment and distances to the classification/decision boundary from SVM

			===Comparison===
			*Unlike AltaCyclic, includes base-specific phasing parameters so can correct raw intensities for T accumulation
			*Does not call an 'N' character for poor quality bases

	==References==		==References==

Srashkin: /* Ibis */

2010-03-12T20:53:07Z

Ibis

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	==Ibis==		==Ibis==

	(~~To be added soon.~~)		*Estimate sequencing chemistry model as a parameter directly from data using statistical learning
			*Training set from Bustard output using raw cluster intensities
			*Used a base caller with SVM classifiers for each cycle that have intensity values of the current cycle as well as the previous and following cycles (if they exist)
			*Data set created by aligning raw reads with mismatches for a fraction of the tiles to a reference sequence
			**Half of this set used as a training set and the other half as a test set used to check results of training
			*Estimate parameters for calculating a quality score given class assignment and distances to the classification/decision boundary from SVM

	==References==		==References==

Srashkin: /* Standard Illumina Base Caller */

2010-03-12T20:46:18Z

Standard Illumina Base Caller

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	==Standard Illumina Base Caller==		==Standard Illumina Base Caller (Bustard)==

	===Sequencing-by-Synthesis (SBS)===		===Sequencing-by-Synthesis (SBS)===
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	*Uses Markov model to determine transition matrix modeling probability of phasing (no new base synthesized), prephasing (two new bases synthesized), and normal incorporation		*Uses Markov model to determine transition matrix modeling probability of phasing (no new base synthesized), prephasing (two new bases synthesized), and normal incorporation
	*Uses transition matrix and observed concentrations of each base to determine concentrations in absence of phasing and reports these as base calls		*Uses transition matrix and observed concentrations of each base to determine concentrations in absence of phasing and reports these as base calls
			**Assumes crosstalk matrix constant for a given sequencing run and that phasing affects all nucleotides in the same way

	===General Noise Factors===		===General Noise Factors===

Srashkin: /* General Noise Factors */

2010-03-12T18:26:51Z

General Noise Factors

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	**Likely caused by overlap in dye emission frequencies		**Likely caused by overlap in dye emission frequencies
	*T Accumulation		*T Accumulation
	**The fluorophores used for thymine ~~show lower removal rate~~ after each iteration ~~and accumulate over the~~ sequencing run		**The fluorophores used for thymine are not always removed properly after each iteration
			**Intensity of T signal increases across sequencing run

	==Alta-Cyclic==		==Alta-Cyclic==

Srashkin: /* General Noise Factors */

2010-03-12T18:24:38Z

General Noise Factors

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	*Crosstalk		*Crosstalk
	**C channel illumination overlaps with A: a C label fluoresces in A channel (similarly G and T overlap)		**C channel illumination overlaps with A: a C label fluoresces in A channel (similarly G and T overlap)
	**Likely caused by overlap in dye emission frequencies		**Likely caused by overlap in dye emission frequencies
			*T Accumulation
			**The fluorophores used for thymine show lower removal rate after each iteration and accumulate over the sequencing run

	==Alta-Cyclic==		==Alta-Cyclic==

Srashkin at 16:09, 26 February 2010

2010-02-26T16:09:44Z

@@ Line 44: / Line 44: @@
 ==Probabilistic Base Calling==
 ==BayesCall==
 ==Swift==
 ==Ibis==

Srashkin at 16:04, 26 February 2010

2010-02-26T16:04:50Z

← Older revision		Revision as of 12:04, 26 February 2010
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	==Alta-Cyclic==		==Alta-Cyclic==
			===Training Stage===
			*Learns run-specific noise patterns according to model and finds optimized solution reducing affect of noise sources using a Support Vector Machine (SVM)
			*Half of training set used for cross-validation

			===Base Calling Stage===
			*Reports all sequences from run with optimized parameters

			===Differences from Standard Illumina Base Caller===
			*Calling parameters optimized empirically and tested to enhance accuracy of each run
			*Calculates phasing parameters based on parametric model
			*Dynamically tracks changes in crosstalk, which disrupt signals in later cycles

	==Probabilistic Base Calling==		==Probabilistic Base Calling==

Srashkin at 16:01, 26 February 2010

2010-02-26T16:01:54Z

← Older revision		Revision as of 12:01, 26 February 2010
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	= Standard Illumina Base Caller =		==Standard Illumina Base Caller==

	= ~~Alta~~-~~Cyclic~~ =		===Sequencing-by-Synthesis (SBS)===

	~~= Probabilistic Base Calling =~~		*DNA sample obtained, containing many copies of same sequences and randomly fragmented
			*Single-stranded DNA fragments attached to slide and amplified so there is a cluster of each fragment
			*DNA polymerase and 4 terminal bases (with distinct fluorescent markers) added
			*Clusters excited by lasers and photos taken in optimal wavelengths for 4 fluorophores
			*Fluorophores and terminators removed and process repeated for L cycles

	= ~~BayesCall~~ =		===Image Analysis===
			*Corrects for imperfect repositioning of camera and aberrations of lens by aligning images to reference from original cycle
			*Signal for each cluster characterized as time series data of fluorescence intensities and noise

	= ~~Swift~~ =		===Base Calling===
			*Converts fluorescence signals into actual sequence data with quality scores
			*Takes intensities of four channels for every cluster in each cycle and determines concentration of each base
			*Renormalizes concentrations by multiplying by ratio of average concentrations in first cycle and current cycle
			*Uses Markov model to determine transition matrix modeling probability of phasing (no new base synthesized), prephasing (two new bases synthesized), and normal incorporation
			*Uses transition matrix and observed concentrations of each base to determine concentrations in absence of phasing and reports these as base calls

	= Ibis =		===General Noise Factors===
			*Phasing
			**Failures in nucleotide incorporation or block removal or incorporation of more than one nucleotide in a particular cycle
			*Fading
			**Decay in fluorescent signal intensity with each cycle
			**Likely attributable to material loss during sequencing
			*Crosstalk
			**C channel illumination overlaps with A: a C label fluoresces in A channel (similarly G and T overlap)
			**Likely caused by overlap in dye emission frequencies

			==Alta-Cyclic==

			==Probabilistic Base Calling==

			==BayesCall==

			==Swift==

			==Ibis==

	(To be added soon.)		(To be added soon.)

	= References =		==References==

	Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R., Hannon, G.J. (2008) Alta-Cyclic: A self-optimizing base caller for next-generation sequencing. ''Nature Methods'' '''5''':679-682		Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R., Hannon, G.J. (2008) Alta-Cyclic: A self-optimizing base caller for next-generation sequencing. ''Nature Methods'' '''5''':679-682