Tag: Error Correction

SEECER 0.1.3 – SEquencing Error CorrEction for Rna reads

SEECER 0.1.3

:: DESCRIPTION

SEECER is an error correction method that removes errors that are introduced during sequencing. Mismatches, insertion or deletions are removed by creating multiple alignments of reads and building HMMs that are used to decide which reads are be corrected. In the provided reference it is shown that error correction with SEECER improves the downstream analysis, especially RNA de novo assembly.

::DEVELOPER

Hai-Son Le , Marcel Schulz , Ziv Bar-Joseph

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SEECER

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 May 1;41(10):e109. doi: 10.1093/nar/gkt215
Probabilistic error correction for RNA sequencing.
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.

SHREC 2.2 – Short Read Error Correction

SHREC 2.2

:: DESCRIPTION

SHREC is a new algorithm for correcting errors in short-read data that uses a generalized suffix trie on the read data as the underlying data structure. Our results show that the method can identify erroneous reads with sensitivity and specificity of over 99% and 96% for simulated data with error rates of up to 3% as well as for real data. Furthermore, it achieves an error correction accuracy of over 80% for simulated data and over 88% for real data. These results are clearly superior to previously published approaches.

::DEVELOPER

Jan Schröder

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SHREC

:: MORE INFORMATION

Citation:

Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, and Bertil Schmidt,
SHREC: A short-read error correction method,
Bioinformatics, 2009 25(17):2157-2163.

Rcorrector 1.0.4 – Error Correction for Illumina RNA-seq Reads

Rcorrector 1.0.4

:: DESCRIPTION

Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux
  • Perl

:: DOWNLOAD

 Rcorrector

:: MORE INFORMATION

Citation

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.
Song L, Florea L.
Gigascience. 2015 Oct 19;4:48. doi: 10.1186/s13742-015-0089-y.

Coral 1.4.1 – Error Correction Algorithm for Correcting reads from DNA sequencing platforms

Coral 1.4.1

:: DESCRIPTION

Coral is an error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer. Coral can utilize also bases distant from the error in the correction process because the whole read is present in the alignment. Coral is easily adjustable to reads produced by different sequencing technologies like Illumina Genome Analyzer and Roche/454 Life Sciences sequencing platforms because the sequencing error model can be defined by the user.

::DEVELOPER

Jan Schröder , Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Coral

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jun 1;27(11):1455-61. Epub 2011 Apr 5.
Correcting errors in short reads by multiple alignments.
Salmela L, Schröder J.

DecGPU 1.0.7 – Distributed short read Error Correction on GPUs

DecGPU 1.0.7

:: DESCRIPTION

DecGPUis the first parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models. Performan evaluation using simulated and real datasets revealed that our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the Hybrid SHREC error correction algorithm The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale datasets.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

  DecGPU

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI“.
BMC Bioinformatics, 2011, 12:85.

 

BFC – High-performance Error Correction for Illumina Resequencing data

BFC v1

:: DESCRIPTION

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BFC

:: MORE INFORMATION

Citation

Bioinformatics. 2015 May 6. pii: btv290.
BFC: correcting Illumina sequencing errors.
Li H

Blue 1.1.3 – Short-read Error-correction tool

Blue 1.1.3

:: DESCRIPTION

Blue is a fast, accurate short-read error-correction tool based on k-mer consensus and context. It will correct both Illumina and 454-like data, and accepts sequence data files in both FASTQ and FASTA formats.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

Blue

:: MORE INFORMATION

Citation

Blue: correcting sequencing errors using consensus and context.
Greenfield P, Duesing K, Papanicolaou A, Bauer DC.
Bioinformatics. 2014 Jun 11. pii: btu368.

Trowel 0.2.0.4 – Error Correction Module for Illumina Sequencing Reads

Trowel 0.2.0.4

:: DESCRIPTION

Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers.

::DEVELOPER

Trowel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

 Trowel

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 29. pii: btu513.
Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D.

Pluribus / PluribusFast – Exploring the Limits of Error Correction Using a Suffix Tree

Pluribus / PluribusFast

:: DESCRIPTION

Pluribus utilizes a suffix tree to identify and correct sequencing errors in next generation sequencing data.

PluribusFast is a more efficient implementation of the Pluribus algorithm.

::DEVELOPER

Pluribus team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • JRE

:: DOWNLOAD

 Pluribus / PluribusFast

:: MORE INFORMATION

Citation

Pluribus – Exploring the Limits of Error Correction Using a Suffix Tree.
Savel D, LaFramboise T, Grama A, Koyuturk M.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Jun 29.