Here’s a brief overview of what Sean has done with the Oly genome assembly front.
- 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 GARM, which relies upon MUMmer and may also include a version of MUMmer (outdated version that led to Sean’s error message?).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
- 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
- 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: http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output/
- Notebook entry
- Second run
- Files (including Mox scripts & output FASTA files) are here: http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Redundans_Output_Try_2/
- Notebook entry
- 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: http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/
- Notebook entry
- Second run
- Files (including Mox scripts & output FASTA files) are here: http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/
- Notebook entry
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