This is the Linux app named Meraculous-2D to run in Linux online whose latest release can be downloaded as Meraculous-v2.2.6.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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Meraculous-2D to run in Linux online
DESCRIPTION
----------------------------------------IMPORTANT: Meraculous-2D has been superseded by HipMer assembler. Get it from here: https://sourceforge.net/projects/hipmer/
-----------------------------------------
Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include:
- Efficient k-mer counting and deBruijn graph traversal
- Two modes of handling of diploid allelic variation
- Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy.
The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server.
Manuscripts in submission:
https://arxiv.org/abs/1703.09852
https://arxiv.org/abs/1608
Features
- Eukaryotic Genome Assembly
- Specialized modes for high- and low-heterozygosity genomesembly
- Built-in distributed execution
- Efficient k-mer space operations
- Single-server and cluster-ready deployment (AWS-ready)
Audience
Science/Research
User interface
Command-line
Programming Language
Perl, C++
This is an application that can also be fetched from https://sourceforge.net/projects/meraculous20/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
