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.

Quartz 0.2 – de novo Quality Score Compression tool

Quartz 0.2

:: DESCRIPTION

Quartz (QUAlity score Reduction at Terabyte scale) is an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Quartz

:: MORE INFORMATION

Citation:

Nat Biotechnol, 33 (3), 240-3 Mar 2015
Quality Score Compression Improves Genotyping Accuracy
Y William Yu, Deniz Yorukoglu , Jian Peng, Bonnie Berger

CAST 1.2.2 – Compression-accelerated BLAST and BLAT

CAST 1.2.2

:: DESCRIPTION

CAST is a set of tools that compress data in a way that allows direct computation on the compressed data. Compression-accelerated BLAST (CaBLAST) and Compression-accelerated BLAT (CaBLAT) are two prototype implementations of alignment and sequence search algorithms that apply “compressive genomics” : i.e., they exploit redundancy in genomic data sets by compressing data in a way that allows direct computation on the compressed data.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ Compiler
  • NCBI C++ Toolkit
  • BLAST+
  • BLAT

:: DOWNLOAD

  CAST

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2012 Jul 10;30(7):627-30. doi: 10.1038/nbt.2241.
Compressive genomics.
Loh PR, Baym M, Berger B.

BARCODE – A fast Lossless Read Compression tool based on Bloom Filters

BARCODE

:: DESCRIPTION

BARCODE achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Python

:: DOWNLOAD

  BARCODE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.
Fast lossless compression via cascading Bloom filters.
Rozov R, Shamir R, Halperin E.

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.

MINCE v0.5.0 ‐ Bucketing-based Reference-free Compression

MINCE v0.5.0

:: DESCRIPTION

MINCE is a technique for encoding collections of short reads so that they can be more effectively compressed via a standard compressor like LZIP.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

MINCE

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24.
Data-dependent bucketing improves reference-free compression of sequencing reads.
Patro R, Kingsford C.

Referee – Rapid, Separable Compression for Sequence Alignments

Referee

:: DESCRIPTION

Referee is a command-line tool that takes sequence alignment SAM files and compresses them in a lossless manner.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Referee

:: MORE INFORMATION

Citation

Darya Filippova, Carl Kingsford (2015).
Rapid, separable compression enables fast analyses of sequence alignments.
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, pages 194-201.

Kpath 0.6.3 – Statistical Reference-based Compression for Short Reads

Kpath 0.6.3

:: DESCRIPTION

Kpath (PathEnc) is a reference-based compression software of short read data sets.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Go

:: DOWNLOAD

 Kpath

:: MORE INFORMATION

Citation

Reference-based compression of short-read sequences using path encoding.
Kingsford C, Patro R.
Bioinformatics. 2015 Feb 2. pii: btv071.

CODOC 0.0.2 – Analysis and Compression of Depth of Coverage Signals

CODOC 0.0.2

:: DESCRIPTION

CODOC is a compressed data format and API for coverage data stemming from sequencing experiments

::DEVELOPER

Niko Popitsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 CODOC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 28. pii: btu362. [Epub ahead of print]
CODOC: Efficient Access, Analysis and Compression of Depth of Coverage Signals.
Popitsch N.