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.
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
Module¶
You can load the modules by:
module load biocontainers
module load masurca
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 -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