FaStore 0.8 – High-performance FASTQ Files Compressor

FaStore 0.8

:: DESCRIPTION

FaStore is a high-performance short FASTQ sequencing reads compressor.

::DEVELOPER

Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

FaStore

:: MORE INFORMATION

Citation

Bioinformatics, 34 (16), 2748-2756 2018 Aug 15
FaStore: A Space-Saving Solution for Raw Sequencing Data
Lukasz Roguski, Idoia Ochoa, Mikel Hernaez , Sebastian Deorowicz

fconv 1.24 – File Conversion

fconv 1.24

:: DESCRIPTION

fconv is a commandline tool concerning manipulating, converting, and analyzing data from different file formats, such as pdb(qt)-, mol2-, dlg-, cif- and sdf-files.

::DEVELOPER

Group of Prof. Dr. G. Klebe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

fconv

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1021-2. doi: 10.1093/bioinformatics/btr055. Epub 2011 Feb 18.
fconv: Format conversion, manipulation and feature computation of molecular data.
Neudert G, Klebe G.

DeeZ 1.9-beta2 – A tool for Compressing SAM/BAM files

DeeZ 1.9-beta2

:: DESCRIPTION

DeeZ (a.k.a. DeeNA-Zip) is a tool for compressing SAM/BAM files, or more formally, a tool which does reference-based compression by local assembly

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 DeeZ

:: MORE INFORMATION

Citation

DeeZ: reference-based compression by local assembly.
Hach F, Numanagić I, Sahinalp SC.
Nat Methods. 2014 Nov;11(11):1082-4. doi: 10.1038/nmeth.3133.

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

Linkdatagen 20130704 – Generates LINKAGE Style Files

Linkdatagen 20130704

:: DESCRIPTION

Linkdatagen is a PERL script that generates LINKAGE style files for ALLEGRO , MERLIN, PREST, MORGAN, PLINK, FEstim, BEAGLE and RELATE using as input genotype calls from Affymetrix SNP chips, Illumina SNP chips, or SNP genotypes inferred from massively parallel sequencing (MPS) data, such as whole exome or whole genome sequence data.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 Linkdatagen

:: MORE INFORMATION

Citation

Bahlo M, Bromhead CJ (2009).
Generating linkage mapping files from Affymetrix SNP chip data.
Bioinformatics 25(15):1961-2.

ExpressConverter 2.1 – Microarray Data Files Transformation Tool

ExpressConverter 2.1

:: DESCRIPTION

ExpressConverter is a file transformation tool that reads microarray data files in a variety of file formats and generates TIGR MultiExperiment Viewer file (.mev) as output so that the microarray data can be uploaded to the database with MADAM and analyzed with MIDAS and MEV.

::DEVELOPER

Dana-Farber Cancer Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows

:: DOWNLOAD

 ExpressConverter

:: MORE INFORMATION

GenescanView 1.2 – Visualize Genescan Files

GenescanView 1.2

:: DESCRIPTION

GenescanView is the free software for the visualization of files generated with automatic ABI sequencers.GenescanView allows to visualize genescan files (.fsa format from ABI PRISM sequencers) and to view the exact peak size.

::DEVELOPER

at CRIBI (University of Padova) by Davide Campagna

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GenescanView

:: MORE INFORMATION

N/A

PDB Editor 090203 – PDB (Protein Data Bank) File Editor

PDB Editor 090203

:: DESCRIPTION

PDB Editor (Protein Data Bank ,PDB, File Editor) is a tool for protein crystallographers to expedite selective edit / data extraction / analysis of their PDB files. It  allows the user to selectively search, select, extract and edit information in parallel.

::DEVELOPER

Jonas Lee

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

PDB Editor

:: MORE INFORMATION

Citation

J. Lee and S.-H. Kim
PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI
Acta Cryst. (2009). D65, 399-402