DeeZ 1.9-beta2 – A tool for Compressing SAM/BAM files

DeeZ 1.9-beta2

:: DESCRIPTION

DeeZ (a.k.a. DeeNA-Zip) is a tool for compressing SAM/BAM files, or more formally, a tool which does reference-based compression by local assembly

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 DeeZ

:: MORE INFORMATION

Citation

DeeZ: reference-based compression by local assembly.
Hach F, Numanagić I, Sahinalp SC.
Nat Methods. 2014 Nov;11(11):1082-4. doi: 10.1038/nmeth.3133.

CoGI – Towards Compressing Genomes as an Image

CoGI

:: DESCRIPTION

CoGI is a novel approach for genome compression, which transforms the genomic sequences to a two-dimensional binary image (or bitmap), then applies a rectangular partition coding algorithm to compress the binary image.

::DEVELOPER

The ADMIS group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 CoGI

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Nov-Dec;12(6):1275-85. doi: 10.1109/TCBB.2015.2430331.
CoGI: Towards Compressing Genomes as an Image.
Xie X, Zhou S, Guan J.

ParaDSRC – Compressing Next Generation Sequencing Data

ParaDSRC

:: DESCRIPTION

ParaDSRC is a high-performance tool for compressing next generation sequencing data using memory-distributed clusters. It uses domain decomposition and message passing interface (MPI) to distributed data on memory-distributed compute nodes.

::DEVELOPER

Parallel Computing and Data Science Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ParaDSRC

:: MORE INFORMATION

Citation

Sandino N. V. Perez and Fahad Saeed*,
A Parallel Algorithm for Compression of Big Next Generation Sequencing Datasets“,
IEEE International Workshop on Parallelism in Bioinformatics (PBio), Proceedings of Parallel and Distributed Processing with Applications (IEEE ISPA-15), Helsinki Finland, August 2015 Tech Report