Purdue University

Commands

• masurca
• build_human_reference.sh
• chromosome_scaffolder.sh
• close_gaps.sh
• close_scaffold_gaps.sh
• correct_with_k_unitigs.sh
• deduplicate_contigs.sh
• deduplicate_unitigs.sh
• eugene.sh
• extract_chrM.sh
• filter_library.sh
• final_polish.sh
• fix_unitigs.sh
• fragScaff.sh
• mega_reads_assemble_cluster.sh
• mega_reads_assemble_cluster2.sh
• mega_reads_assemble_polish.sh
• mega_reads_assemble_ref.sh
• parallel_delta-filter.sh
• polca.sh
• polish_with_illumina_assembly.sh
• recompute_astat_superreads.sh
• recompute_astat_superreads_CA8.sh
• reconcile_alignments.sh
• refine.sh
• resolve_trio.sh
• run_ECR.sh
• samba.sh
• splitScaffoldsAtNs.sh

Module

You can load the modules by:

module load biocontainers
module load masurca

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run masurca on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=masurca
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers masurca