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, and Chromosome scaffolder.

The MaSuRCA assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches. Since version 3.2.1 it supports hybrid assembly with short Illumina reads and long noisy PacBio/MinION data.

References:

• Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013 Nov 1;29(21):2669-77.
• Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Yorke JA, Dvorak J, Salzberg S. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research. 2017 Jan 1:066100.
• Zimin AV, Salzberg SL. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS computational biology. 2020 Jun 26;16(6):e1007981.
• Zimin AV, Salzberg SL. The SAMBA tool uses long reads to improve the contiguity of genome assemblies. PLoS computational biology. 2022 Feb 4;18(2):e1009860.

• MaSuRCA on GitHub

• Module Name: masurca (see the modules page for more information)
• Multithreaded using the -t flag.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive -c 32
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load masurca

[user@cn3144 ~]$ masurca -t $SLURM_CPUS_PER_TASK -i /path_to/pe_R1.fa,/path_to/pe_R2.fa

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. masurca.sh). For example:

#!/bin/bash
set -e
module load masurca
masurca -t $SLURM_CPUS_PER_TASK -i /path_to/pe_R1.fa,/path_to/pe_R2.fa -r /path_to/nanopore.fastq.gz

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] masurca.sh

Create a swarmfile (e.g. masurca.swarm). For example:

masurca -t $SLURM_CPUS_PER_TASK -i sample1_pe_R1.fa,sample1_pe_R2.fa -r sample1_nanopore.fastq.gz
masurca -t $SLURM_CPUS_PER_TASK -i sample2_pe_R1.fa,sample2_pe_R2.fa -r sample2_pacbio.fastq.gz
masurca -t $SLURM_CPUS_PER_TASK -i sample3_pe_R1.fa,sample3_pe_R2.fa -r sample3_nanopore.fasta.gz
masurca -t $SLURM_CPUS_PER_TASK -i sample4_pe_R1.fa,sample4_pe_R2.fa -r sample4_pacbio.fasta.gz

Submit this job using the swarm command.

swarm -f masurca.swarm [-g #] [-t #] --module masurca