libCSAM – Lossy Compression of Quality Scores in Genomic data

libCSAM

:: DESCRIPTION

libCSAM will contain several C++ codes for compress,decompress, and access each of the fields of any SAM format file.

::DEVELOPER

Rodrigo Cánovas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 libCSAM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2.
Lossy compression of quality scores in genomic data.
Cánovas R1, Moffat A, Turpin A.

HaMMLET – Fast Bayesian Hidden Markov Model with Wavelet Compression

HaMMLET

:: DESCRIPTION

HaMMLET is a fast Forward-Backward Gibbs sampler for Bayesian inference on Hidden Markov Models (HMM). It uses the Haar wavelet transform to dynamically compress the data based on the current variance sample in each iteration.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 HaMMLET

:: MORE INFORMATION

Citation

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.
Wiedenhoeft J, Brugel E, Schliep A.
PLoS Comput Biol. 2016 May 13;12(5):e1004871. doi: 10.1371/journal.pcbi.1004871.

SNPack 1.0 – Compression and fast Retrieval of SNP data

SNPack 1.0

:: DESCRIPTION

SNPack is a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies.

::DEVELOPER

SYSTEMS BIOLOGY AND BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SNPack

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu495.
Compression and fast retrieval of SNP data.
Sambo F, Di Camillo B, Toffolo G, Cobelli C.

DNAcompact 20130829 – Genome Compression algorithm with/without Reference

DNAcompact 20130829

:: DESCRIPTION

DNA-COMPACT is a software of DNA COMpression based on a pattern-aware contextual modeling technique.

::DEVELOPER

DNAcompact team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 DNAcompact

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 25;8(11):e80377. doi: 10.1371/journal.pone.0080377. eCollection 2013.
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.
Li P1, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X.

samcomp 0.10 – Compression for SAM/BAM file format

samcomp 0.10

:: DESCRIPTION

samcomp is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.

::DEVELOPER

James K. Bonfield (jkb@sanger.ac.uk), Matt Mahoney

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 samcomp

:: 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

LW-FQZip – Light-weight reference-based compression of FASTQ data

LW-FQZip

:: DESCRIPTION

LW-FQZip is a lossless light-weight reference-based compression tool for FASTQ data.

::DEVELOPER

Zexuan ZHU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LW-FQZip

:: MORE INFORMATION

Citation

Light-weight reference-based compression of FASTQ data.
Zhang Y, Li L, Yang Y, Yang X, He S, Zhu Z.
BMC Bioinformatics. 2015 Jun 9;16(1):188. doi: 10.1186/s12859-015-0628-7.

LFQC 1.1 – Lossless Compression Algorithm for FASTQ Files

LFQC 1.1

:: DESCRIPTION

LFQC is a new lossless non-reference based fastq compression algorithm.

::DEVELOPER

Sanguthevar Rajasekaran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Ruby

:: DOWNLOAD

 LFQC

:: MORE INFORMATION

Citation

LFQC: A lossless compression algorithm for FASTQ files.
Nicolae M, Pathak S, Rajasekaran S.
Bioinformatics. 2015 Jun 20. pii: btv384.

oculus 0.1.2 – Faster Sequence Alignment by Compression

oculus 0.1.2

:: DESCRIPTION

Oculus is a bioinformatic algorithm designed to increase sequence alignment speed for redundant input. It acts as a wrapper around any existing alignment algorithm capable of producing SAM-formatted output.

::DEVELOPER

The Michigan Center for Translational Pathology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Oculus

:: MORE INFORMATION

BMC Bioinformatics. 2012 Nov 13;13:297. doi: 10.1186/1471-2105-13-297.
Oculus: faster sequence alignment by streaming read compression.
Veeneman BA1, Iyer MK, Chinnaiyan AM.

Kolmogorov – Compression-based Classification of Biological Sequences and Structures

Kolmogorov

:: DESCRIPTION

Kolmogorov is a multistep approach to classify and cluster Biological Sequences and Structures, via Compression.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl
  • BioPerl

:: DOWNLOAD

 Kolmogorov

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 13;8:252.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
Ferragina P1, Giancarlo R, Greco V, Manzini G, Valiente G.

FRESCO – A Framework for Referential Sequence Compression

FRESCO

:: DESCRIPTION

FRESCO is a general open-source framework to compress large amounts of biological sequence data.

::DEVELOPER

Wissensmanagement in der Bioinformatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FRESCO

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1275-88.
FRESCO: Referential compression of highly similar sequences.
Wandelt S, Leser U.