Tag: Convert

iConvert – Convert Genotype Allele Formats

iConvert

:: DESCRIPTION

The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).

::DEVELOPER

iConvert team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • Python

:: DOWNLOAD

 iConvert

:: MORE INFORMATION

Citation

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.

Tbl2KnownGene – Convert NCBI.tbl to UCSC knownGene.txt data file

Tbl2KnownGene

:: DESCRIPTION

Tbl2KnownGene is a wrapper tool that parses the contents of a NCBI .tbl annotation table and produces a UCSC Known Genes annotation table.

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Tbl2KnownGene

:: MORE INFORMATION

Citation

Bioinformation. 2014 Aug 30;10(8):544-7. doi: 10.6026/97320630010544. eCollection 2014.
Tbl2KnownGene: A command-line program to convert NCBI.tbl to UCSC knownGene.txt data file.
Bai Y

PRIDE Converter 2.5.7 – Converts Mass Spectrometry Data into PRIDE XML

PRIDE Converter 2.5.7

:: DESCRIPTION

PRIDE Converter 2 converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service.

::DEVELOPER

PRIDE Converter Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PRIDE Converter

:: MORE INFORMATION

Citation

Barsnes et. al:
PRIDE Converter: making proteomics data-sharing easy
Nat Biotechnol. 2009 Jul;27(7):598-9.

Cote RG & Griss J, et al.,
The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Mol Cell Proteomics. 2012 Sep 4.

Convert2Sbml / Convert2Matlab – Convert Metabolic Network Source files into SBML / MATLAB files

Convert2Sbml / Convert2Matlab

:: DESCRIPTION

Convert2Sbml / Convert2Matlab is the Java tool to convert various metabolic network source files into SBML / MATLAB files.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Convert2Sbml / Convert2Matlab

:: MORE INFORMATION

AgileFileConverter 20130213 – Converts Varaint data File Format

AgileFileConverter 20130213

:: DESCRIPTION

AgileFileConverter converts varaint data in tab delimited text files, typically supplied by commercial NGS service providers, into the format used by AgileGeneFilter, AgileVariantViewer and AgileFileViewer

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileFileConverter

:: MORE INFORMATION

Illumina2Affy v1/v2/v3 – Converts Illumina files into Affymetrix-style file.

Illumina2Affy v1/v2/v3

:: DESCRIPTION

Illumina2Affy converts Illumina files containing ONE/MULTIPLE individual’s genotype data of the format shown below into an Affymetrix-style file.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

   Illumina2Affy

:: MORE INFORMATION

CrossMap 0.5.3 – Convert Genome Coordinates Between Assemblies

CrossMap 0.5.3

:: DESCRIPTION

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.

::DEVELOPER

CrossMap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • C++ Compiler

:: DOWNLOAD

  CrossMap

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.
CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Zhao H1, Sun Z, Wang J, Huang H, Kocher JP, Wang L.

ms2ms.pl – Convert the Output of Hudson’s Makesample software into Microsatellite data

ms2ms.pl

:: DESCRIPTION

ms2ms.pl converts the output of Hudson’s makesample software into microsatellite data. The output could be directly analyzed by MSA.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 ms2ms.pl

:: MORE INFORMATION

Citation

SREENIVASA R. PIDUGU andCHRISTIAN SCHLÖTTERER
ms2ms.pl: a PERL script for generating microsatellite data
Molecular Ecology Notes Volume 6, Issue 2, pages 580–581, June 2006

cnv2wiggle – Convert CNV Details to wig and generate a BED file

cnv2wiggle

:: DESCRIPTION

The cnv2wiggle perl script will create a bed track for ploidy segments different from 2 and a gwiggle plot of the relative coverae. These files can be opened in IGV. This script doesn’t include hypervariable regions

::DEVELOPER

Complete Genomics, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 cnv2wiggle

:: MORE INFORMATION

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