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.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/masurca
Home page: https://github.com/alekseyzimin/masurca

Versions

  • 4.0.9

  • 4.1.0

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

Example job

Warning

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=masurca
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load masurca/XXXX ### you can run *module avail masurca* to check all available versions