Tag: Error Corrector

HECTOR 1.0 – A Parallel Homopolymer Spectrum based 454 Error Corrector

HECTOR 1.0

:: DESCRIPTION

HECTOR is a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In this algorithm, for the first time we have investigated a novel homopolymer spectrum based approach to handle homopolymer insertions or deletions, which are the dominant sequencing errors in 454 short-reads.

::DEVELOPER

HECTOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HECTOR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 6;15(1):131. [Epub ahead of print]
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J.

Acacia 1.53 – Error-corrector for Pyrosequenced Amplicon Reads

Acacia 1.53

:: DESCRIPTION

The Acacia program was implemented to correct errors in pyrosequenced amplicons quickly and with high specificity.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

Acacia

:: REQUIREMENTS

  • Linux / Windows / MacOSX
  • Java

:: DOWNLOAD

 Acacia

:: MORE INFORMATION

Citation

Fast, accurate error-correction of amplicon pyrosequences using Acacia.
Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW.
Nat Methods. 2012 Apr 27;9(5):425-6. doi: 10.1038/nmeth.1990.

Musket 1.1 – Parallel and Scalable Multistage K-mer Spectrum based Error Corrector for Illumina Sequence data

Musket 1.1

:: DESCRIPTION

Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time.

::DEVELOPER

Yongchao Liu, Dr.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Musket

:: MORE INFORMATION

Citation

Yongchao Liu, Jan Schroeder and Bertil Schmidt:
“ Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data“.
Bioinformatics, 2013, 29(3): 308-315