Tag: Next Generation Sequencing

ebGenotyping 2.0.1 – Genotyping and SNP Detection using Next Generation Sequencing Data

ebGenotyping 2.0.1

:: DESCRIPTION

ebGenotyping is a novel statistical model to fit the observed non-reference allele frequency data, and utilize the empirical Bayes method for both genotyping and SNP detection, where an ECM algorithm is implemented to estimate the model parameters.

::DEVELOPER

Na You and Gongyi Huang <53hgy at 163.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

 ebGenotyping

:: MORE INFORMATION

Citation:

An Empirical Bayes Method for Genotyping and SNP Detection Using Multi-sample Next-generation Sequencing Data.
Huang G, Wang S, Wang X, You N.
Bioinformatics. 2016 Jul 4. pii: btw409.

NGSView 0.91 – Editor for Next-generation Sequencing data

NGSView 0.91

:: DESCRIPTION

NGSView (Next Generation Sequence View) is a software for high-throughput sequencing technologies introduce novel demands on tools available for data analysis.

::DEVELOPER

Erik Arner, PhD

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 NGSView

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):125-6. Epub 2009 Oct 24.
NGSView: an extensible open source editor for next-generation sequencing data.
Arner E, Hayashizaki Y, Daub CO.

SRMA 0.1.15 – Sequence Re-alignment for Next Generation Sequencing

SRMA 0.1.15

:: DESCRIPTION

SRMA (Short Read Micro re-Aligner) is a software package that performs sequence re-alignment for next generation sequencing technology.It fixes artifacts introduced by aligning each read independently, significantly reducing the false positive detection, while cleaning insertions and deletions.

::DEVELOPER

Nils Homer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

SRMA

:: MORE INFORMATION

Citation:

Homer N, Nelson SF.
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.
Genome Biol. 2010 Oct 8;11(10):R99 PMID: 20932289

DNAA 0.1.2 – Analysis Package for Short-read Next Generation Sequencing

DNAA 0.1.2

:: DESCRIPTION

DNAA (DNA Analysis) is an analysis package for short-read next generation sequencing. It comprises a suite of tools. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.

::DEVELOPER

Nils Homer

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DNAA

:: MORE INFORMATION

License

GNU General Public License (GPL)