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.

MetaCRAM – Lossless Compression Tool for Metagenomic Reads

MetaCRAM

:: DESCRIPTION

MetaCRAM is a pipeline for taxonomy identification and lossless compression of FASTA-format metagenomic reads.  It integrates algorithms for taxonomy identification, read alignment, assembly, and finally, a reference-based compression method in a parallel manner.

::DEVELOPER

Minji Kim

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl
  • Java

:: DOWNLOAD

  MetaCRAM

:: MORE INFORMATION

Citation

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.
Kim M, Zhang X, Ligo JG, Farnoud F, Veeravalli VV, Milenkovic O.
BMC Bioinformatics. 2016 Feb 19;17(1):94. doi: 10.1186/s12859-016-0932-x