Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. It uses the disk streaming k-mer counting algorithm contained in the GATB library, and inserts solid k-mers in a bloom-filter. The correction procedure is similar to the Musket multistage approach. Bloocoo yields similar results while requiring far less memory: as an example, it can correct whole human genome re-sequencing reads at 70 x coverage with less than 4GB of memory.
G. Benoit, D. Lavenier, C. Lemaitre, G. Rizk. (2015) Bloocoo, a memory efficient read corrector. Inria-HAL.
Bloocoo is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:
|MacOS-X 10.9 or above.
(Intel 64bit processors)
|Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)
For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.
|Bloocoo tool is fully written in C++.||Download|
Bloocoo binaries and source code are covered by the Affero GPL version 3 license.