Tag: Pyrosequencing

Deep Threshold Tool / Rosetta Tool – Analysis of Ultra-deep Pyrosequencing and Cloning

Deep Threshold Tool / Rosetta Tool

:: DESCRIPTION

Deep Threshold Tool / Rosetta Tool is web server for analysis of ultra-deep pyrosequencing and cloning based sequencing of the basic core promoter/precore/core region of hepatitis B virus using newly developed bioinformatics tools.

::DEVELOPER

Hepatitis Virus Diversity Research Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Yousif*, M., Bell*, T. G., Mudawi, H., Glebe, D. and Kramvis, A. (2014)
Analysis of ultra-deep pyrosequencing and cloning based sequencing of the basic core promoter/precore/core region of hepatitis B virus using newly developed bioinformatics tools.
PLoS ONE 9(4): e95377.

NoDe – Error-correcting Algorithm for 454 Pyrosequencing Reads

NoDe

:: DESCRIPTION

NoDe (Noise Detector) is a new error correction algorithm which was trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read.

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NoDe

:: MORE INFORMATION

Citation:

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.
Mysara M, Leys N, Raes J, Monsieurs P.
BMC Bioinformatics. 2015 Mar 15;16(1):88.

CorQ 20130619 – Quality Score based Identification and Correction of Pyrosequencing Errors

CorQ 20130619

:: DESCRIPTION

CorQ (Correction through Quality) is a new algorithm which utilizes the inherent base quality in a sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion (indel) errors.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CorQ

:: MORE INFORMATION

Citation

PLoS One. 2013 Sep 5;8(9):e73015. doi: 10.1371/journal.pone.0073015. eCollection 2013.
Quality score based identification and correction of pyrosequencing errors.
Iyer S1, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI.

PyroCleaner 1.3 – Clean 454 Pyrosequencing Reads in order to ease the Assembly Process

PyroCleaner 1.3

:: DESCRIPTION

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.

::DEVELOPER

the bioinformatic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PyroCleaner

:: MORE INFORMATION

Citation

Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149