Meraculous

Description

Distributed and scalable assembler for eukaryotic genomes.

Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of meraculous and load default version of meraculous as

module avail meraculous/ # list available modules
module load meraculous   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail meraculous

and choose explicit version you want to use.

Documentation

http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2014/12/Manual.pdf

Homepage

http://jgi.doe.gov/data-and-tools/meraculous/ https://sourceforge.net/projects/meraculous20/