Purdue University

masurca

Link to section 'Introduction' of 'masurca' Introduction

The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.

Docker hub: https://hub.docker.com/r/staphb/masurca
Home page: https://github.com/alekseyzimin/masurca

Link to section 'Versions' of 'masurca' Versions

• 4.0.9

Link to section 'Commands' of 'masurca' 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

Link to section 'Module' of 'masurca' Module

You can load the modules by:

module load biocontainers
module load masurca

Link to section 'Example job' of 'masurca' Example job

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