sidneymbell/shasta

De novo assembly from Oxford Nanopore reads.

Shasta long read assembler

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The complete user documentation is available here.

For quick start information see here.

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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).

An initial implementation of the Shasta assembler is complete and functional, but significant improvements in several areas are possible. As currently implemented, it 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.

The accuracy of assembled sequence is being analyzed. Early indications are that Shasta is similar or better in assembly quality when compared to other long read assemblers.

Acknowledgments

The Shasta software uses various external software packages. See here for more information.

Reporting Security Issues

Please note: If you believe you have found a security issue, please responsibly disclose by contacting [email protected].

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The complete user documentation is available here.

For quick start information see here.

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