GTRAC V0.1.4 – Genotype Random Access Compressor

GTRAC V0.1.4

:: DESCRIPTION

GTRAC is a new algorithm that achieves significant compression ratios while allowing fast random access over the compressed database.

::DEVELOPER

Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

GTRAC

:: MORE INFORMATION

Citation

GTRAC: fast retrieval from compressed collections of genomic variants.
Tatwawadi K, et al.
Bioinformatics 2016. PMID 27587665 Free PMC article.

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

iDoComp 1.2 – Compression Scheme for Assembled Genomes

iDoComp 1.2

:: DESCRIPTION

iDoComp is an algorithm to compress re-sequenced assembled genomes, i.e., genomes for which an assembled genome of the same species already exists

::DEVELOPER

 Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 iDoComp

:: MORE INFORMATION

Citation

iDoComp: A Compression Scheme for Assembled Genomes.
Ochoa I, Hernaez M, Weissman T.
Bioinformatics. 2014 Oct 24. pii: btu698.

YALFF v0.1.0 – Yet Another Lossy Fastq Filter

YALFF v0.1.0

:: DESCRIPTION

YALFF is a tool for quality scores compression by smoothing leading to improved compressibility of FASTQ files.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

YALFF

:: MORE INFORMATION

Citation

BMC Bioinformatics, 20 (Suppl 9), 302 2019 Nov 22
Better Quality Score Compression Through Sequence-Based Quality Smoothing
Yoshihiro Shibuya, Matteo Comin

OrthoXML 0.3 / SeqXML 0.4 – XML standards for Orthology and Sequence Information

OrthoXML 0.3 / SeqXML 0.4

:: DESCRIPTION

OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format.

The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a ‘Z’, this error will be detected automatically by any XML validator.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

OrthoXML  / SeqXML

:: MORE INFORMATION

Split fasta – Split large FASTA file into smaller files

Split fasta

:: DESCRIPTION

Split fasta file into smaller segments. This is useful if you have a large FASTA file that needs to be split into smaller files.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  Split fasta

:: MORE INFORMATION

genio 1.0.12 – Genetics Input/Output Functions

genio 1.0.12

:: DESCRIPTION

The genio (GENetics I/O) package provides easy-to-use and efficient readers and writers for formats in genetics research.

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

genio

:: MORE INFORMATION

Gro2mat – A package to efficiently read Gromacs output in Matlab

Gro2mat

:: DESCRIPTION

gro2mat is a package that allows fast and easy access to Gromacs output files from Matlab.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 Gro2mat

:: MORE INFORMATION

Citation

J Comput Chem. 2014 Jul 30;35(20):1528-31. doi: 10.1002/jcc.23650. Epub 2014 Jun 12.
Gro2mat: a package to efficiently read gromacs output in MATLAB.
Dien H1, Deane CM, Knapp B.

HapZipper – Compression Scheme for HapMap Phase III Phased Data

HapZipper

:: DESCRIPTION

HapZipper is a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 HapZipper

:: MORE INFORMATION

Citation

HapZipper: sharing HapMap populations just got easier.
Chanda P, Elhaik E, Bader JS.
Nucleic Acids Res. 2012 Nov 1;40(20):e159. doi: 10.1093/nar/gks709.