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.

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.