SPRING v1.0.1 – FASTQ Compressor

SPRING v1.0.1

:: DESCRIPTION

SPRING is a compression tool for Fastq files.

::DEVELOPER

Tsachy (Itschak) Weissman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Conda
  • C COmpiler

:: DOWNLOAD

SPRING

:: MORE INFORMATION

Citation

Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T.
SPRING: a next-generation compressor for FASTQ data.
Bioinformatics. 2019 Aug 1;35(15):2674-2676. doi: 10.1093/bioinformatics/bty1015. PMID: 30535063; PMCID: PMC6662292.

FastqCLS – FASTQ Compressor for Long-read Sequencing

FastqCLS

:: DESCRIPTION

FastqCLS is a robust FASTQ-specific compressor for recent generation data via score-based reordering.

:: DEVELOPER

FastqCLS team

:: REQUIREMENTS

  • Linux / Window
  • Python

:: DOWNLOAD

FastqCLS

:: MORE INFORMATION

Citation

Lee D, Song G.
FastqCLS: a FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model.
Bioinformatics. 2021 Oct 8:btab696. doi: 10.1093/bioinformatics/btab696. Epub ahead of print. PMID: 34623374.

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

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.

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

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

QVZ / QVZ2 0.1 – A Lossy Compressor for Quality Scores in Genomic Data

QVZ / QVZ2 0.1

:: 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 / QVZ2

:: 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.

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.

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