Tag: Error

MORPHEUS – Identify Residues in Predicted Models with a large Error

MORPHEUS

:: DESCRIPTION

MORPHEUS is a tool to identify and rebuild residues in predicted models with a large error. The error in predicted models is estimated using the average pairwise geometric distance per residue computed among selected lowest energy models. This error distribution among residues is employed to guide the rebuilding process that focuses on more error-prone residues of the coarse-grain models.

::DEVELOPER

Structural Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MORPHEUS

:: MORE INFORMATION

Citation

Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1522-34. doi: 10.1107/S0907444912037961. Epub 2012 Oct 18.
Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing.
Shrestha R1, Simoncini D, Zhang KY.

MESA – MOSLA Error Simulator

MESA

:: DESCRIPTION

MESA is a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms.

::DEVELOPER

Distributed Systems and Intelligent Computing

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MESA

:: MORE INFORMATION

Citation

Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D.
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors.
Bioinformatics. 2020 Jun 1;36(11):3322-3326. doi: 10.1093/bioinformatics/btaa140. PMID: 32129840; PMCID: PMC7267826.

Reptile 1.1 – Short Read Error Correction

Reptile 1.1

:: DESCRIPTION

Reptile (Representative tiling) corrects sequencing errors in short reads (32bp ~ 150bp) generated by next-gen sequencing platforms, e.g. Illumina.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Perl

:: DOWNLOAD

 Reptile

:: MORE INFORMATION

Citation

X. Yang, K. Dorman and S. Aluru,
“Reptile: Representative tiling for short read error correction”,
Bioinformatics, 26(20), 2526-2533, 2010.

GIGI-Check 1.06 – Detection of Mendelian Consistent Genotyping Errors

GIGI-Check 1.06

:: DESCRIPTION

GIGI-Check is a C++ program to detect Mendelian consistent genotyping errors of dense markers in pedigree data.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GIGI-Check

:: MORE INFORMATION

Citation:

Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2014)
Detection of Mendelian Consistent Genotyping Errors in Pedigrees.
Genetic Epidemiology 38(4):291-299

ACE 1.01 – Accurate Correction of Errors using K-mer tries

ACE 1.01

:: DESCRIPTION

ACE corrects substitution errors in an Illumina archive using a k-mer trie.

::DEVELOPER

ACE team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux  /MacOsX
  • C++

:: DOWNLOAD

  ACE

:: MORE INFORMATION

Citation

ACE: Accurate Correction of Errors using K-mer tries.
Sheikhizadeh S, de Ridder D.
Bioinformatics. 2015 May 28. pii: btv332.

GRR 1.2.1.41 – Detect Pedigree Errors

GRR 1.2.1.41

:: DESCRIPTION

GRR (Graphical Representation of Relationships) is a Windows-based application for detecting pedigree errors via graphically inspecting the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GRR

:: MORE INFORMATION

If you decide to use GRR, please take a minute to register.

HiTEC 20110131 – Accurate Error Correction in High-throughput Sequencing data

HiTEC 20110131

:: DESCRIPTION

HiTEC (High Throughput Error Correction) , an algorithm that provides a highly accurate, robust and fully automated method to correct reads produced by high-throughput sequencing methods. The approach provides significantly higher accuracy than previous methods. It is time and space efficient and works very well for all read lengths, genome sizes and coverage levels.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HiTEC

:: MORE INFORMATION

Citation

L. Ilie, F. Fazayeli, S. Ilie,
HiTEC: accurate error correction in high-throughput sequencing data,
Bioinformatics 27(3) (2011) 295 — 302.