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Shasta long read assembler

De novo assembler for long reads, optimized for Oxford Nanopore (ONT) reads.

🆕 Mode 3 assembly: presentation of assembly results

🆕 Mode 3 assembly: usage notes


Shasta development continues in this fork.

New releases will appear in the Releases page of this repository. Previous releases (up to 0.10.0) are available from the Release page of pre-fork repository chanzuckerberg/shasta.


The complete user documentation is available here.

For quick start information see here.

The main paper describing Shasta and its methods and results is Shafin et al., Nature Biotechnology 2020. Reads from this paper are available here. The assembly results are here.

Requests for help: please file GitHub issues to report problems, request help, or ask questions. Please keep each issue on a single topic when possible.


Main features of the Shasta long read assembler:

Computational methods used by the Shasta assembler include:

See this documentation page for more information on computational methods.

Acknowledgments

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


The complete user documentation is available here.

For quick start information see here.