Tag: Mutation Detection

Illuminator 20110419 – Mutation Detection using Short-read Clonal Sequencing

Illuminator 20110419

:: DESCRIPTION

Illuminator is a new sequence alignment program for the output from Illumina GA-II clonal sequencers. It is aimed primarily at kilobase-sized reference regions, as would typically be used in the context of mutation detection.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

Illuminator

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 Illuminator

:: MORE INFORMATION

Citation

Carr IM, Morgan JE, Diggle CP, Sheridan EG, Markham AF, Logan CV, Inglehearn CF, Taylor GR, Bonthron DT.
Illuminator, a desktop program for mutation detection using short-read clonal sequencing.
Genomics 2011 Oct;98(4):302-9.

Xplorer 2.4.3 – Chromatogram Editor with Mutation Detection

Xplorer 2.4.3

:: DESCRIPTION

Xplorer is a stand alone chromatogram editor with mutation detection.

  • View multiple Chromatograms.
  • Edit any Base Call.
  • Export individual Fasta sequence files from each chromatogram.
  • Export Fasta DB from selected chromatograms.
  • Trim sequences.
  • Display base call differences and detect Hetrozygote & Homozygotes within multiple chromatograms.

::DEVELOPER

dnaTools, Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

Xplorer

:: MORE INFORMATION

EBCall – Empirical Bayesian framework for Mutation Detection from Cancer Genome Sequencing data

EBCall

:: DESCRIPTION

EBCall (Empirical Bayesian mutation Calling) is a software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.

::DEVELOPER

Yuichi Shiraishi (yshira@hgc.jp) ,Kenichi Chiba

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • samtools
  • R package
  • C++ Compiler
  • The VGAM package for R

:: DOWNLOAD

 EBCall

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Apr;41(7):e89. doi: 10.1093/nar/gkt126. Epub 2013 Mar 6.
An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data.
Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S.