:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
MFCompress is a compression tool for FASTA and multi-FASTA files. In comparison to gzip and applied to multi-FASTA files, MFCompress can provide additional average compression gains of almost 50%, i.e.,it potentially doubles the available storage, although at the cost of some more computation time.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Armando J. Pinho, and Diogo Pratas.
“MFCompress: a compression tool for FASTA and multi-FASTA data.”
Bioinformatics 30.1 (2014): 117-118.DOI: dx.doi.org/10.1093/bioinformatics/btt594.
:: DESCRIPTION
MENT is a set of tools for lossless compression of microarray images, however, it can be used in other kind of images such as medical, RNAi, etc.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Luís M. O. Matos, António J. R. Neves, Armando J. Pinho,
“Lossy-to-lossless compression of biomedical images based on image decomposition”,
in Digital Signal Processing, (chapter proposal accepted on December 4, 2014).
:: DESCRIPTION
MAFCO is a lossless compression tool specifically designed to compress MAF (Multiple Alignment Format) files.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MAFCO: A Compression Tool for MAF Files.
Matos LM, Neves AJ, Pratas D, Pinho AJ.
PLoS One. 2015 Mar 27;10(3):e0116082. doi: 10.1371/journal.pone.0116082.
:: DESCRIPTION
The smallWig tool provides compression/decompression for WIG files.
::DEVELOPER
Zhiying Wang, Tsachy (Itschak) Weissman
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
smallWig: Parallel Compression of RNA-seq WIG Files.
Wang Z, Weissman T, Milenkovic O.
Bioinformatics. 2015 Sep 30. pii: btv561.
:: DESCRIPTION
UST is a bioinformatics tool for constructing a spectrum-preserving string set (SPSS) representation from sets of k-mers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Amatur Rahman and Paul Medvedev,
“Representation of k-mer sets using spectrum-preserving string sets”,
in submission.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
iDoComp: A Compression Scheme for Assembled Genomes.
Ochoa I, Hernaez M, Weissman T.
Bioinformatics. 2014 Oct 24. pii: btu698.
:: DESCRIPTION
cbc is a program for compression and decompression of aligned reads presented in a SAM file.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
