MaSuRCA assembler

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).
If you use MaSuRCA in your work, please cite our paper:

Zimin, A. et al. The MaSuRCA genome Assembler. Bioinformatics (2013). doi:10.1093/bioinformatics/btt476

UPDATE (July 2016): the MaSuRCA system now includes a new module to build mega-reads for hybrid Pacbio (or Nanopore) + Illumina de novo assembly, which is described in a forthcoming paper.
One can supply either Pacbio or Nanopore reads (not both) as PACBIO=file.fa or NANOPORE=file.fa in the configuration file. All Pacbio or Nanopore reads must be in a single fasta file! To obtain the latest SOURCE CODE of MaSuRCA and compilation instructions, see this page. Please check out the MaSuRCA blog at and MaSuRCA github page at From now on all development and release announcements will be posted there.

Download MaSuRCA

Genomes assembled with MaSuRCA

  • Ancestral wheat D, Aegilops tauschii, 4.25Gb genome, joint with Jan Dvorak and Mingcheng Guo, UC-Davis, Pacbio+Illumina data, paper preprint.
  • Loblolly pine, Pinus taeda, 22Gb genome, joint with David Neale and Chuck Langley, UC-Davis, and Pinerefseq consortium. Illumina data.
  • Indian cow, Bos indicus, joint with USDA-ARS, 454/Illumina mixed data.
  • Rhesus macaque, Macaca mulatta, joint with Robert Norgren, University of Nebraska. Sanger/Illumina mixed data.
  • Water Buffalo, Bubalus bubalus, joint with USDA-ARS and CASPUR, Italy. 454/Illumina mixed data.
  • Domestic cat, Felis felis, joint with Wes Warren, Washington University, St. Louis. Sanger/454/Illumina mixed data.
  • American bison, Bison bison. 454/Illumina mixed data.
  • Philippine tarsier, Tarsius syrichta, joint with Wes Warren, Washington University, St. Louis. Sanger/Illumina mixed data.
  • Cardiocondyla ant, 454/Illumina mixed data.
  • Fire ant, joint with Sasha Mikheleev, OIST, Japan. 454/Illumina mixed data.
  • Stalk-eyed fly, Teleopsis dalmanni, joint with Gerry Wilkinson, University of Maryland. 454/Illumina mixed data.