Genome assembly and quality · Software
MaSuRCA
Assembles genomes from short Illumina reads, alone or combined with long reads, using super-reads.
What MaSuRCA is
MaSuRCA (Maryland Super Read Cabog Assembler) is a genome assembly and analysis toolkit designed to construct high-continuity sequence assemblies. The software package incorporates the primary assembler alongside the QuORUM error corrector for Illumina reads, the POLCA consensus polishing tool, a reference-assisted chromosome scaffolder, the SAMBA long-read scaffolder, the jellyfish k-mer counter, and the MUMmer aligner.
The toolkit addresses the computational complexity of assembling genomes by transforming high-coverage short Illumina reads into longer synthetic fragments termed super-reads, effectively reducing total read volume whilst maintaining sequence information. MaSuRCA combines the advantages of de Bruijn graph and Overlap-Layout-Consensus (OLC) paradigms. It also enables hybrid assemblies by using short Illumina reads to correct high-error long reads generated by PacBio or Oxford Nanopore sequencing through a mega-reads approach.
How it works
MaSuRCA begins by counting k-mers with jellyfish and error-correcting Illumina reads using QuORUM. The assembler constructs a de Bruijn graph—using a user-defined k-mer size or an automatically selected value based on read characteristics and GC content—to extend unambiguous paths into super-reads. When long PacBio or Oxford Nanopore reads are provided, the software employs a mega-reads algorithm that uses the short-read data to replace the high-error long reads with accurate synthetic sequences over one or two correction passes.
The resulting super-reads and corrected mega-reads are supplied to an overlap-layout-consensus assembler, typically the Celera Assembler (CABOG), or optionally Flye when assembling hybrid long-read datasets with at least 15x long-read coverage. For large genomes assembled from Illumina data alone, the SOAPdenovo2 module can be selected for faster contig generation and scaffolding. Post-assembly workflows can deploy SAMBA to bridge intra-scaffold gaps with long reads, the chromosome scaffolder to order contigs against a reference genome, and POLCA to polish base errors using read alignments from BWA-MEM.
Key facts
- Supported OS
- Linux (tested on Fedora 12+, RedHat 5/6, CentOS 5/6, Ubuntu 12 LTS+, SUSE Linux 16+)
- CPU Architecture
- Intel and AMD x64
- Mandatory Input
- Illumina paired-end reads (FASTQ)
- Optional Inputs
- Illumina mate pairs, PacBio reads, Oxford Nanopore reads, Sanger/454 reads (.frg), reference FASTA
- Output Formats
- FASTA (scaffolds, contigs, corrected reads), VCF (POLCA variants)
- Integrated Components
- QuORUM, POLCA, SAMBA, Celera Assembler (CABOG), Flye, jellyfish, MUMmer, SOAPdenovo2
- Grid Engine Support
- SGE and SLURM
What you can use it for
- De novo short-read assembly
- Assembles bacterial, plant, insect, and mammalian genomes using Illumina paired-end reads with optional mate-pair jumping libraries.
- Hybrid genome assembly
- Merges high-coverage Illumina data with error-prone Oxford Nanopore or PacBio SMRT reads using the mega-reads algorithm.
- Reference-guided chromosome scaffolding
- Orders, orients, and breaks putative misassemblies in contigs using chromosome-level references and long-read alignment data.
- Long-read gap closure
- Closes intra-scaffold gaps and resolves contig orientation errors in existing assemblies using SAMBA and long reads.
- Assembly consensus polishing
- Polishes base and indel errors in long-read assemblies using POLCA with short Illumina or PacBio HiFi reads.
Run it here
Ask the research agent and it runs MaSuRCA as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
Try asking
“Assemble this bacterial genome from my paired-end reads with MaSuRCA.”
Strengths and limits
Good at
- Combines the computational efficiency of de Bruijn graphs with the long-range resolution of overlap-layout-consensus assembly.
- Reduces data complexity by collapsing short Illumina reads into longer, unique super-reads prior to final assembly.
- Executes hybrid error correction for long reads in parallel across SGE or SLURM compute clusters.
- Includes dedicated supplementary tools for reference-based chromosome scaffolding, long-read gap filling, and variant-based polishing.
Watch out for
- Requires Illumina paired-end sequencing reads as a mandatory prerequisite for all assembly workflows.
- Demands at least 50x coverage in Illumina paired-end reads before PacBio or Oxford Nanopore data can be integrated.
- Operates exclusively on Linux systems and is unsupported when installed via Bioconda due to package conflicts.
- Demands substantial computing hardware for large genomes, requiring up to 2 terabytes of RAM and 10 terabytes of disk space for a 30 Gb plant genome.
Questions
Can I run MaSuRCA online without installing it?
Ask the research agent and it runs MaSuRCA as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
What licence is MaSuRCA under?
GPL-3.0. The terms are published at https://github.com/alekseyzimin/masurca.
Can MaSuRCA run on long reads alone?
No. Illumina paired-end sequencing data is mandatory for all assemblies, even when Oxford Nanopore or PacBio reads are supplied.
Should Illumina reads be pre-processed or quality-trimmed before running MaSuRCA?
Third-party pre-processing, trimming, cleaning, or error correction should be avoided, as altering the raw reads tends to deteriorate the final assembly quality.
When can Flye be used within MaSuRCA?
Flye can be selected for final contigging and scaffolding only in hybrid assemblies that combine Illumina paired-end reads with Oxford Nanopore or PacBio reads having at least 15x coverage, without mate-pair or other legacy libraries.
How does the chromosome scaffolder identify misassemblies?
It aligns reads to query contigs and compares them to a reference sequence, identifying putative misassemblies where contigs diverge from the reference and breaking contigs at locations failing coverage thresholds.
What external software does POLCA depend on?
POLCA requires the BWA-MEM aligner to be installed and accessible on the system PATH to align polishing reads to the target assembly.
How to cite it
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013 Nov 1;29(21):2669-77.
Written from MaSuRCA's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.