KIC 0.2 – K-mer Index Compressor Software Suite

KIC 0.2

:: DESCRIPTION

KIC is a FASTQ compressor based on a new integer-mapped k-mer indexing method.

::DEVELOPER

Y.Sun Lab

:: SCREENSHOTS

KIC

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

 KIC

:: MORE INFORMATION

Citation

A FASTQ compressor based on integer-mapped k-mer indexing for biologist.
Zhang Y, Patel K, Endrawis T, Bowers A, Sun Y.
Gene. 2016 Mar 15;579(1):75-81. doi: 10.1016/j.gene.2015.12.053.

ORCOM 1.0 – Compressor of Sequencing Reads

ORCOM 1.0

:: DESCRIPTION

ORCOM (Overlapping Reads COmpression with Minimizers) is a compressor of sequencing reads. It takes as an input FASTQ files (possibly gzipped) and stores the DNA symbols of each read in a highly-compressed form.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ORCOM

:: MORE INFORMATION

Citation

Disk-based compression of data from genome sequencing.
Grabowski S, Deorowicz S, Roguski Ł.
Bioinformatics. 2014 Dec 22. pii: btu844.

GDC 2.0 / TEST_RA 0.3 – Genome Differential Compressor

GDC 2.0 / TEST_RA 0.3

:: DESCRIPTION

GDC is a utility designed for compression of genome collections from the same species.

TEST_RA is an application that performs tests of the random access queries to the compressed archive.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 GDC  / TEST_RA

:: MORE INFORMATION

Citation

GDC 2: Compression of large collections of genomes.
Deorowicz S, Danek A, Niemiec M.
Sci Rep. 2015 Jun 25;5:11565. doi: 10.1038/srep11565.

Bioinformatics. 2011 Nov 1;27(21):2979-86. doi: 10.1093/bioinformatics/btr505. Epub 2011 Sep 5.
Robust relative compression of genomes with random access.
Deorowicz S1, Grabowski S.

QVZ – A Lossy Compressor for Quality Scores in Genomic Data

QVZ

:: DESCRIPTION

QVZ (Quality Value Zip) is a lossy compression algorithm for storing quality values associated with DNA sequencing.

::DEVELOPER

Greg Malysa, Mikel Hernaez, Idoia Ochoa, Milind Rao, and Karthik Ganesan at Stanford University.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QVZ

:: MORE INFORMATION

Citation

QVZ: lossy compression of quality values.
Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.
Bioinformatics. 2015 May 28. pii: btv330.

SACO – Sequence Alignment COmpressor

SACO

:: DESCRIPTION

SACO is a lossless compression tool for the sequences alignments found in the MAF files. SACO was designed to handle the DNA bases and gap symbols that can be found in MAF files.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • C Compiler

:: DOWNLOAD

 SACO

:: MORE INFORMATION

Citation

Luís M. O. Matos, Diogo Pratas, and Armando J. Pinho,
A Compression Model for DNA Multiple Sequence Alignment Blocks”,
IEEE Transactions on Information Theory, volume 59, number 5, pages 3189-3198, May 2013. DOI: dx.doi.org/10.1109/TIT.2012.2236605

Fastqz 1.5 / Fqzcomp 4.6 – FASTQ File Compressor

Fastqz 1.5 / Fqzcomp 4.6

:: DESCRIPTION

fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. It may be used with a reference genome for better compression.

Fqzcomp is a basic fastq compressor, designed primarily for high performance. 

::DEVELOPER

Matt Mahoney

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • C++ Compiler

:: DOWNLOAD

 Fastqz , Fqzcomp

:: MORE INFORMATION

Citation

Bonfield JK, Mahoney MV (2013)
Compression of FASTQ and SAM Format Sequencing Data. 
PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190

NGC 0.0.1 – Compressor for High-throughput Sequencing data

NGC 0.0.1

:: DESCRIPTION

NGC is a compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.

::DEVELOPER

Niko Popitsch the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 NGC

:: MORE INFORMATION

Citation

Niko Popitsch and Arndt von Haeseler
NGC: lossless and lossy compression of aligned high-throughput sequencing data
Nucl. Acids Res. (7 January 2013) 41 (1): e27.