Shasta

Software Description:

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).

Software Home Page: Shasta

Software Documentation:

To run this software in a Linux environment on LCC,
run the command(s):

#To load module
module load ccs/shasta/shasta-0.1.0

#To unload module
module unload ccs/shasta/shasta-0.1.0