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The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.

Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

As currently implemented, Shasta can run an assembly of a human genome at coverage around 60x in about 5 hours using a single, large machine (AWS instance type x1.32xlarge, with 128 virtual processors and 1952 GB of memory). The compute cost of such an assembly is around $20 at AWS spot market or reserved prices.

Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers - see this paper for an extensive analysis.

Environment Modules

Run module spider shasta to find out what environment modules are available for this application.

System Variables

  • HPC_SHASTA_DIR - installation directory
  • HPC_SHASTA_BIN - executable directory