AYB 2.11 – Advanced Base Calling for Next Generation Sequencing Machines

AYB 2.11

:: DESCRIPTION

AYB (All your base) is a base caller for the Illumina Genome Analyzer, using an explicit statistical model of how errors occur during sequencing to produce more accurate reads from the raw intensity data.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AYB

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Feb 29;13(2):R13. [Epub ahead of print]
All your base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.

DeepNano – Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads

DeepNano

:: DESCRIPTION

DeepNano is a base caller for MinION, the smallest DNA sequencer currently available.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DeepNano

:: MORE INFORMATION

Citation

PLoS One. 2017 Jun 5;12(6):e0178751. doi: 10.1371/journal.pone.0178751. eCollection 2017.
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.
Boža V1, Brejová B1, Vinař T1.

Rsolid 0.9-31 – Normalization and Base Calling for ABI SOLiD data

Rsolid 0.9-31

:: DESCRIPTION

Rsolid is a R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles.
Rafael Irizarry’s Lab

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

  Rsolid

:: MORE INFORMATION

Citation

Nat Methods. 2010 May;7(5):336-7. doi: 10.1038/nmeth0510-336.
Intensity normalization improves color calling in SOLiD sequencing.
Wu H, Irizarry RA, Bravo HC.

BlindCall 1.0 – Ultra-fast Base-calling of Second-generation Sequencing data by Blind Deconvolution

BlindCall 1.0

:: DESCRIPTION

BlindCall is a simple and ultra-fast non-probabilistic base-calling method for Illumina high-throughput sequencing data based on blind deconvolution.

::DEVELOPER

Héctor Corrada Bravo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 BlindCall

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1214-9. doi: 10.1093/bioinformatics/btu010. Epub 2014 Jan 9.
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.
Ye C1, Hsiao C, Corrada Bravo H.

BM-BC 1.0 – Bayesian method of Base Calling for Solexa Sequence data

BM-BC 1.0

:: DESCRIPTION

BM-BC is a Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian method builds on a hierarchical model that accounts for three sources of noise in the data, which are known to affect the accuracy of the base calls: fading, phasing, and cross-talk between channels.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 BM-BC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 13:S6. doi: 10.1186/1471-2105-13-S13-S6. Epub 2012 Aug 24.
BM-BC: a Bayesian method of base calling for Solexa sequence data.
Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S.