<![CDATA[BOL: Shasta long read assembler]]> https://bioinformaticsonline.com/bookmarks/view/40531/shasta-long-read-assembler? https://bioinformaticsonline.com/bookmarks/view/40531/shasta-long-read-assembler Tue, 14 Jan 2020 06:47:07 -0600 https://bioinformaticsonline.com/bookmarks/view/40531/shasta-long-read-assembler <![CDATA[Shasta long read assembler]]> 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).

More at https://chanzuckerberg.github.io/shasta/index.html

Address of the bookmark: https://github.com/chanzuckerberg/shasta

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40531/shasta-long-read-assembler#item-annotation-3755 Thu, 06 Feb 2020 08:13:43 -0600 https://bioinformaticsonline.com/bookmarks/view/40531/shasta-long-read-assembler#item-annotation-3755 <![CDATA[Comment by Neel]]> Latest release are here https://github.com/chanzuckerberg/shasta/releases

]]> Neel