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.

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.