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.
This package is built using SPACK and optimized for AVX, AVX2 and AVX512 CPUs. To use the optimized version, you need to add source /etc/profile.d/zlmod.sh to your submit script before loading any modules. By default, the AVX2 optimized version (head node is Haswell CPU) is in your path. The AVX2 optimized version will run on Skylake (enge, im2080, chem, health) and Cascade Lake (hawkcpu, hawkmem, hawkgpu, infolab) CPUs but not on Ivybridge (debug) CPUs.
| Version | module name |
|---|---|
| 3.4.2 | masurca/3.4.2 |
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 high error PacBio/MinION data.
Citation for MaSuRCA: Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013 Nov 1;29(21):2669-77.
Citation for MaSuRCA hybrid assembler: 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.
For more information visit https://github.com/alekseyzimin/masurca