Software: Meraculous
Description
Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It is hybrid k-mer/read-based approach 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.
Available Versions
| Unspecified: | 2.2.6 |
|---|
Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster 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.
Home page: https://jgi.doe.gov/data-and-tools/software-tools/meraculous/
Commands
- run_meraculous.sh
- blastMapAnalyzer2.pl
- bmaToLinks.pl
- _bubbleFinder2.pl
- bubblePopper.pl
- bubbleScout.pl
- contigBias.pl
- divide_it.pl
- fasta_splitter.pl
- findDMin2.pl
- gapDivider.pl
- gapPlacer.pl
- haplotyper.Naive.pl
- haplotyper.pl
- histogram2.pl
- kmerHistAnalyzer.pl
- loadBalanceMers.pl
- meraculous4h.pl
- meraculous.pl
- N50.pl
- _oNo4.pl
- oNo7.pl
- optimize2.pl
- randomList2.pl
- scaffold2contig.pl
- scaffReportToFasta.pl
- screen_list2.pl
- spanner.pl
- splinter.pl
- splinter_scaffolds.pl
- split_and_validate_reads.pl
- test_dependencies.pl
- unique.pl
Module
You can load the modules by:
module load biocontainers
module load meraculous
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run meraculous on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=meraculous
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers meraculous