Here’s a brief overview of what Sean has done with the Oly genome assembly front.

Metassembler

• Assemble his BGI assembly and Platanus assembly? Confusing terms here; not sure what he means.

• Failed due to 32-bit vs. 64-bit installation of MUMmer. He didn’t have the chance to re-compile MUMmer as 64-bit. However, a recent MUMmer announcement suggests that MUMmer can now handle genomes of unlimited size.

• I believe he was planning on using (or was using?) GARM, which relies upon MUMmer and may also include a version of MUMmer (outdated version that led to Sean’s error message?).

• Notebook entry

Canu

• Assemble UW PacBio data (filenames beginning with m170211, m170315, m170308, and m170301).

• Files (including Mox scripts, Pilon contig polishing, & output FASTA files) are here: http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Canu_Output/

• Notebook entry

Redundans

• Assembled raw Illumina reads provided by BGI (filenames beginning with 15114 and 16103) & UW PacBio data (filenames beginning with m170211, m170315, m170308, and m170301).

• Ran this two times.

• First run

  • Files (does NOT include Mox scripts!) are here: https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output/

  • Notebook entry

• Second run

  • Files (including Mox scripts & output FASTA files) are here: https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output_Try_2/

  • Notebook entry

Platanus

• Assembled raw Illumina reads provided by BGI (beginning with 151114 and 160103).

• Ran this two times.

• First run

  • Files (including Mox scripts & output FASTA files) are here: https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/

  • Notebook entry

• Second run

  • Files (including Mox scripts & output FASTA files) are here: https://owl.fish.washington.edu/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/

  • Notebook entry